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Gene prediction - Wikipedia
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id="toc-Neural_networks-sublist" class="vector-toc-list"> </ul> </li> </ul> </li> <li id="toc-Combined_approaches" class="vector-toc-list-item vector-toc-level-1 vector-toc-list-item-expanded"> <a class="vector-toc-link" href="#Combined_approaches"> <div class="vector-toc-text"> <span class="vector-toc-numb">3</span> <span>Combined approaches</span> </div> </a> <ul id="toc-Combined_approaches-sublist" class="vector-toc-list"> </ul> </li> <li id="toc-Comparative_genomics_approaches" class="vector-toc-list-item vector-toc-level-1 vector-toc-list-item-expanded"> <a class="vector-toc-link" href="#Comparative_genomics_approaches"> <div class="vector-toc-text"> <span class="vector-toc-numb">4</span> <span>Comparative genomics approaches</span> </div> </a> <button aria-controls="toc-Comparative_genomics_approaches-sublist" class="cdx-button cdx-button--weight-quiet cdx-button--icon-only vector-toc-toggle"> <span class="vector-icon mw-ui-icon-wikimedia-expand"></span> <span>Toggle Comparative genomics approaches subsection</span> </button> <ul id="toc-Comparative_genomics_approaches-sublist" class="vector-toc-list"> <li id="toc-Multiple_informants" class="vector-toc-list-item vector-toc-level-2"> <a class="vector-toc-link" href="#Multiple_informants"> <div class="vector-toc-text"> <span class="vector-toc-numb">4.1</span> <span>Multiple informants</span> </div> </a> <ul id="toc-Multiple_informants-sublist" class="vector-toc-list"> </ul> </li> </ul> </li> <li id="toc-Pseudogene_prediction" class="vector-toc-list-item vector-toc-level-1 vector-toc-list-item-expanded"> <a class="vector-toc-link" href="#Pseudogene_prediction"> <div class="vector-toc-text"> <span class="vector-toc-numb">5</span> <span>Pseudogene prediction</span> </div> </a> <ul id="toc-Pseudogene_prediction-sublist" class="vector-toc-list"> </ul> </li> <li id="toc-Metagenomic_gene_prediction" class="vector-toc-list-item vector-toc-level-1 vector-toc-list-item-expanded"> <a class="vector-toc-link" href="#Metagenomic_gene_prediction"> <div class="vector-toc-text"> <span class="vector-toc-numb">6</span> <span>Metagenomic gene prediction</span> </div> </a> <ul id="toc-Metagenomic_gene_prediction-sublist" class="vector-toc-list"> </ul> </li> <li id="toc-See_also" class="vector-toc-list-item vector-toc-level-1 vector-toc-list-item-expanded"> <a class="vector-toc-link" href="#See_also"> <div class="vector-toc-text"> <span class="vector-toc-numb">7</span> <span>See also</span> </div> </a> <ul id="toc-See_also-sublist" class="vector-toc-list"> </ul> </li> <li id="toc-References" class="vector-toc-list-item vector-toc-level-1 vector-toc-list-item-expanded"> <a class="vector-toc-link" href="#References"> <div class="vector-toc-text"> <span class="vector-toc-numb">8</span> <span>References</span> </div> </a> <ul id="toc-References-sublist" class="vector-toc-list"> </ul> </li> <li id="toc-External_links" class="vector-toc-list-item vector-toc-level-1 vector-toc-list-item-expanded"> <a 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interwiki-bs mw-list-item"><a href="https://bs.wikipedia.org/wiki/Predvi%C4%91anje_gena" title="Predviđanje gena – Bosnian" lang="bs" hreflang="bs" data-title="Predviđanje gena" data-language-autonym="Bosanski" data-language-local-name="Bosnian" class="interlanguage-link-target"><span>Bosanski</span></a></li><li class="interlanguage-link interwiki-ca mw-list-item"><a href="https://ca.wikipedia.org/wiki/Predicci%C3%B3_de_gens" title="Predicció de gens – Catalan" lang="ca" hreflang="ca" data-title="Predicció de gens" data-language-autonym="Català" data-language-local-name="Catalan" class="interlanguage-link-target"><span>Català</span></a></li><li class="interlanguage-link interwiki-de mw-list-item"><a href="https://de.wikipedia.org/wiki/Genvorhersage" title="Genvorhersage – German" lang="de" hreflang="de" data-title="Genvorhersage" data-language-autonym="Deutsch" data-language-local-name="German" class="interlanguage-link-target"><span>Deutsch</span></a></li><li class="interlanguage-link interwiki-es badge-Q17437798 badge-goodarticle mw-list-item" title="good article badge"><a href="https://es.wikipedia.org/wiki/Predicci%C3%B3n_de_genes" title="Predicción de genes – Spanish" lang="es" hreflang="es" data-title="Predicción de genes" data-language-autonym="Español" data-language-local-name="Spanish" class="interlanguage-link-target"><span>Español</span></a></li><li class="interlanguage-link interwiki-fa mw-list-item"><a href="https://fa.wikipedia.org/wiki/%DA%98%D9%86%E2%80%8C%DB%8C%D8%A7%D8%A8%DB%8C" title="ژنیابی – Persian" lang="fa" hreflang="fa" data-title="ژنیابی" data-language-autonym="فارسی" data-language-local-name="Persian" class="interlanguage-link-target"><span>فارسی</span></a></li><li class="interlanguage-link interwiki-fr mw-list-item"><a href="https://fr.wikipedia.org/wiki/Pr%C3%A9diction_de_g%C3%A8nes" title="Prédiction de gènes – French" lang="fr" hreflang="fr" data-title="Prédiction de gènes" data-language-autonym="Français" 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href="/wiki/File:Gene_structure.svg" class="mw-file-description"><img src="//upload.wikimedia.org/wikipedia/commons/thumb/1/11/Gene_structure.svg/350px-Gene_structure.svg.png" decoding="async" width="350" height="55" class="mw-file-element" srcset="//upload.wikimedia.org/wikipedia/commons/thumb/1/11/Gene_structure.svg/525px-Gene_structure.svg.png 1.5x, //upload.wikimedia.org/wikipedia/commons/thumb/1/11/Gene_structure.svg/700px-Gene_structure.svg.png 2x" data-file-width="480" data-file-height="75" /></a><figcaption>Structure of a <a href="/wiki/Eukaryotic" class="mw-redirect" title="Eukaryotic">eukaryotic</a> gene</figcaption></figure> <p>In <a href="/wiki/Computational_biology" title="Computational biology">computational biology</a>, <b>gene prediction</b> or <b>gene finding</b> refers to the process of identifying the regions of genomic DNA that encode <a href="/wiki/Genes" class="mw-redirect" title="Genes">genes</a>. This includes protein-coding <a href="/wiki/Gene" title="Gene">genes</a> as well as <a href="/wiki/RNA_gene" class="mw-redirect" title="RNA gene">RNA genes</a>, but may also include prediction of other functional elements such as <a href="/wiki/Regulatory_regions" class="mw-redirect" title="Regulatory regions">regulatory regions</a>. Gene finding is one of the first and most important steps in understanding the genome of a species once it has been <a href="/wiki/Sequencing" title="Sequencing">sequenced</a>. </p><p>In its earliest days, "gene finding" was based on painstaking experimentation on living cells and organisms. Statistical analysis of the rates of <a href="/wiki/Homologous_recombination" title="Homologous recombination">homologous recombination</a> of several different genes could determine their order on a certain <a href="/wiki/Chromosome" title="Chromosome">chromosome</a>, and information from many such experiments could be combined to create a <a href="/wiki/Genetic_map" class="mw-redirect" title="Genetic map">genetic map</a> specifying the rough location of known genes relative to each other. Today, with comprehensive genome sequence and powerful computational resources at the disposal of the research community, gene finding has been redefined as a largely computational problem. </p><p>Determining that a sequence is functional should be distinguished from determining <a href="/wiki/Protein_function_prediction" title="Protein function prediction">the function</a> of the gene or its product. Predicting the function of a gene and confirming that the gene prediction is accurate still demands <i><a href="/wiki/In_vivo" title="In vivo">in vivo</a></i> experimentation<sup id="cite_ref-Sleator2010_1-0" class="reference"><a href="#cite_note-Sleator2010-1"><span class="cite-bracket">[</span>1<span class="cite-bracket">]</span></a></sup> through <a href="/wiki/Gene_knockout" title="Gene knockout">gene knockout</a> and other assays, although frontiers of <a href="/wiki/Bioinformatics" title="Bioinformatics">bioinformatics</a> research <sup id="cite_ref-2" class="reference"><a href="#cite_note-2"><span class="cite-bracket">[</span>2<span class="cite-bracket">]</span></a></sup> are making it increasingly possible to predict the function of a gene based on its sequence alone. </p><p>Gene prediction is one of the key steps in <a href="/wiki/Genome_annotation" class="mw-redirect" title="Genome annotation">genome annotation</a>, following <a href="/wiki/Sequence_assembly" title="Sequence assembly">sequence assembly</a>, the filtering of non-coding regions and repeat masking.<sup id="cite_ref-Yandell2012_3-0" class="reference"><a href="#cite_note-Yandell2012-3"><span class="cite-bracket">[</span>3<span class="cite-bracket">]</span></a></sup> </p><p>Gene prediction is closely related to the so-called 'target search problem' investigating how <a href="/wiki/DNA-binding_proteins" class="mw-redirect" title="DNA-binding proteins">DNA-binding proteins</a> (<a href="/wiki/Transcription_factors" class="mw-redirect" title="Transcription factors">transcription factors</a>) locate specific <a href="/wiki/Binding_sites" class="mw-redirect" title="Binding sites">binding sites</a> within the <a href="/wiki/Genome" title="Genome">genome</a>.<sup id="cite_ref-redding2013_4-0" class="reference"><a href="#cite_note-redding2013-4"><span class="cite-bracket">[</span>4<span class="cite-bracket">]</span></a></sup><sup id="cite_ref-sokolov2005_5-0" class="reference"><a href="#cite_note-sokolov2005-5"><span class="cite-bracket">[</span>5<span class="cite-bracket">]</span></a></sup> Many aspects of structural gene prediction are based on current understanding of underlying <a href="/wiki/Biochemistry" title="Biochemistry">biochemical</a> processes in the <a href="/wiki/Cell_(biology)" title="Cell (biology)">cell</a> such as gene <a href="/wiki/Transcription_(genetics)" class="mw-redirect" title="Transcription (genetics)">transcription</a>, <a href="/wiki/Translation_(biology)" title="Translation (biology)">translation</a>, <a href="/wiki/Protein%E2%80%93protein_interaction" title="Protein–protein interaction">protein–protein interactions</a> and <a href="/wiki/Regulation_of_gene_expression" title="Regulation of gene expression">regulation processes</a>, which are subject of active research in the various <a href="/wiki/Omics" title="Omics">omics</a> fields such as <a href="/wiki/Transcriptomics" class="mw-redirect" title="Transcriptomics">transcriptomics</a>, <a href="/wiki/Proteomics" title="Proteomics">proteomics</a>, <a href="/wiki/Metabolomics" title="Metabolomics">metabolomics</a>, and more generally <a href="/wiki/Structural_genomics" title="Structural genomics">structural</a> and <a href="/wiki/Functional_genomics" title="Functional genomics">functional genomics</a>. </p> <meta property="mw:PageProp/toc" /> <div class="mw-heading mw-heading2"><h2 id="Empirical_methods">Empirical methods</h2><span class="mw-editsection"><span class="mw-editsection-bracket">[</span><a href="/w/index.php?title=Gene_prediction&action=edit&section=1" title="Edit section: Empirical methods"><span>edit</span></a><span class="mw-editsection-bracket">]</span></span></div> <p>In empirical (similarity, homology or evidence-based) gene finding systems, the target genome is searched for sequences that are similar to extrinsic evidence in the form of the known <a href="/wiki/Expressed_sequence_tags" class="mw-redirect" title="Expressed sequence tags">expressed sequence tags</a>, <a href="/wiki/Messenger_RNA" title="Messenger RNA">messenger RNA</a> (mRNA), <a href="/wiki/Protein" title="Protein">protein</a> products, and homologous or orthologous sequences. Given an mRNA sequence, it is trivial to derive a unique genomic DNA sequence from which it had to have been <a href="/wiki/Transcription_(genetics)" class="mw-redirect" title="Transcription (genetics)">transcribed</a>. Given a protein sequence, a family of possible coding DNA sequences can be derived by reverse translation of the <a href="/wiki/Genetic_code" title="Genetic code">genetic code</a>. Once candidate DNA sequences have been determined, it is a relatively straightforward algorithmic problem to efficiently search a target genome for matches, complete or partial, and exact or inexact. Given a sequence, local alignment algorithms such as <a href="/wiki/BLAST_(biotechnology)" title="BLAST (biotechnology)">BLAST</a>, <a href="/wiki/FASTA" title="FASTA">FASTA</a> and <a href="/wiki/Smith%E2%80%93Waterman_algorithm" title="Smith–Waterman algorithm">Smith-Waterman</a> look for regions of similarity between the target sequence and possible candidate matches. Matches can be complete or partial, and exact or inexact. The success of this approach is limited by the contents and accuracy of the sequence database. </p><p>A high degree of similarity to a known messenger RNA or protein product is strong evidence that a region of a target genome is a protein-coding gene. However, to apply this approach systemically requires extensive sequencing of mRNA and protein products. Not only is this expensive, but in complex organisms, only a subset of all genes in the organism's genome are expressed at any given time, meaning that extrinsic evidence for many genes is not readily accessible in any single cell culture. Thus, to collect extrinsic evidence for most or all of the genes in a complex organism requires the study of many hundreds or thousands of <a href="/wiki/List_of_distinct_cell_types_in_the_adult_human_body" class="mw-redirect" title="List of distinct cell types in the adult human body">cell types</a>, which presents further difficulties. For example, some human genes may be expressed only during development as an embryo or fetus, which might be difficult to study for ethical reasons. </p><p>Despite these difficulties, extensive transcript and protein sequence databases have been generated for human as well as other important model organisms in biology, such as mice and yeast. For example, the <a href="/wiki/RefSeq" title="RefSeq">RefSeq</a> database contains transcript and protein sequence from many different species, and the <a href="/wiki/Ensembl" class="mw-redirect" title="Ensembl">Ensembl</a> system comprehensively maps this evidence to human and several other genomes. It is, however, likely that these databases are both incomplete and contain small but significant amounts of erroneous data. </p><p>New high-throughput <a href="/wiki/Transcriptome" title="Transcriptome">transcriptome</a> sequencing technologies such as <a href="/wiki/RNA-Seq" title="RNA-Seq">RNA-Seq</a> and <a href="/wiki/ChIP-sequencing" class="mw-redirect" title="ChIP-sequencing">ChIP-sequencing</a> open opportunities for incorporating additional extrinsic evidence into gene prediction and validation, and allow structurally rich and more accurate alternative to previous methods of measuring <a href="/wiki/Gene_expression" title="Gene expression">gene expression</a> such as <a href="/wiki/Expressed_sequence_tag" title="Expressed sequence tag">expressed sequence tag</a> or <a href="/wiki/DNA_microarray" title="DNA microarray">DNA microarray</a>. </p><p>Major challenges involved in gene prediction involve dealing with sequencing errors in raw DNA data, dependence on the quality of the <a href="/wiki/Sequence_assembly" title="Sequence assembly">sequence assembly</a>, handling short reads, <a href="/wiki/Frameshift_mutation" title="Frameshift mutation">frameshift mutations</a>, <a href="/wiki/Overlapping_gene" title="Overlapping gene">overlapping genes</a> and incomplete genes. </p><p>In prokaryotes it's essential to consider <a href="/wiki/Horizontal_gene_transfer" title="Horizontal gene transfer">horizontal gene transfer</a> when searching for gene <a href="/wiki/Sequence_homology" title="Sequence homology">sequence homology</a>. An additional important factor underused in current gene detection tools is existence of gene clusters — <a href="/wiki/Operon" title="Operon">operons</a> (which are functioning units of <a href="/wiki/DNA" title="DNA">DNA</a> containing a cluster of <a href="/wiki/Gene" title="Gene">genes</a> under the control of a single <a href="/wiki/Promoter_(genetics)" title="Promoter (genetics)">promoter</a>) in both prokaryotes and eukaryotes. Most popular gene detectors treat each gene in isolation, independent of others, which is not biologically accurate. </p> <div class="mw-heading mw-heading2"><h2 id="Ab_initio_methods"><i>Ab initio</i> methods</h2><span class="mw-editsection"><span class="mw-editsection-bracket">[</span><a href="/w/index.php?title=Gene_prediction&action=edit&section=2" title="Edit section: Ab initio methods"><span>edit</span></a><span class="mw-editsection-bracket">]</span></span></div> <p>Ab Initio gene prediction is an intrinsic method based on gene content and signal detection. Because of the inherent expense and difficulty in obtaining extrinsic evidence for many genes, it is also necessary to resort to <i><a href="/wiki/Ab_initio" title="Ab initio">ab initio</a></i> gene finding, in which the <a href="/wiki/Genomic" class="mw-redirect" title="Genomic">genomic</a> <a href="/wiki/DNA_sequence" class="mw-redirect" title="DNA sequence">DNA sequence</a> alone is systematically searched for certain tell-tale signs of protein-coding genes. These signs can be broadly categorized as either <i>signals</i>, specific sequences that indicate the presence of a gene nearby, or <i>content</i>, statistical properties of the protein-coding sequence itself. <i>Ab initio</i> gene finding might be more accurately characterized as gene <i>prediction</i>, since extrinsic evidence is generally required to conclusively establish that a putative gene is functional. </p> <figure class="mw-default-size" typeof="mw:File/Thumb"><a href="/wiki/File:Gene_Prediction.png" class="mw-file-description"><img src="//upload.wikimedia.org/wikipedia/commons/thumb/2/2b/Gene_Prediction.png/220px-Gene_Prediction.png" decoding="async" width="220" height="165" class="mw-file-element" srcset="//upload.wikimedia.org/wikipedia/commons/thumb/2/2b/Gene_Prediction.png/330px-Gene_Prediction.png 1.5x, //upload.wikimedia.org/wikipedia/commons/thumb/2/2b/Gene_Prediction.png/440px-Gene_Prediction.png 2x" data-file-width="1408" data-file-height="1056" /></a><figcaption>This picture shows how Open Reading Frames (ORFs) can be used for gene prediction. Gene prediction is the process of determining where a coding gene might be in a genomic sequence. Functional proteins must begin with a Start codon (where DNA transcription begins), and end with a Stop codon (where transcription ends). By looking at where those codons might fall in a DNA sequence, one can see where a functional protein might be located. This is important in gene prediction because it can reveal where coding genes are in an entire genomic sequence. In this example, a functional protein can be discovered using ORF3 because it begins with a Start codon, has multiple amino acids, and then ends with a Stop codon, all within the same reading frame.<sup id="cite_ref-6" class="reference"><a href="#cite_note-6"><span class="cite-bracket">[</span>6<span class="cite-bracket">]</span></a></sup></figcaption></figure> <p>In the genomes of <a href="/wiki/Prokaryotes" class="mw-redirect" title="Prokaryotes">prokaryotes</a>, genes have specific and relatively well-understood <a href="/wiki/Promoter_(biology)" class="mw-redirect" title="Promoter (biology)">promoter</a> sequences (signals), such as the <a href="/wiki/Pribnow_box" title="Pribnow box">Pribnow box</a> and <a href="/wiki/Transcription_factor" title="Transcription factor">transcription factor</a> <a href="/wiki/Binding_site" title="Binding site">binding sites</a>, which are easy to systematically identify. Also, the sequence coding for a protein occurs as one contiguous <a href="/wiki/Open_reading_frame" title="Open reading frame">open reading frame</a> (ORF), which is typically many hundred or thousands of <a href="/wiki/Base_pair" title="Base pair">base pairs</a> long. The statistics of <a href="/wiki/Stop_codon" title="Stop codon">stop codons</a> are such that even finding an open reading frame of this length is a fairly informative sign. (Since 3 of the 64 possible codons in the genetic code are stop codons, one would expect a stop codon approximately every 20–25 codons, or 60–75 base pairs, in a <a href="/wiki/Random_sequence" title="Random sequence">random sequence</a>.) Furthermore, protein-coding DNA has certain <a href="/wiki/Frequency" title="Frequency">periodicities</a> and other statistical properties that are easy to detect in a sequence of this length. These characteristics make prokaryotic gene finding relatively straightforward, and well-designed systems are able to achieve high levels of accuracy. </p><p><i>Ab initio</i> gene finding in <a href="/wiki/Eukaryotes" class="mw-redirect" title="Eukaryotes">eukaryotes</a>, especially complex organisms like humans, is considerably more challenging for several reasons. First, the promoter and other regulatory signals in these genomes are more complex and less well-understood than in prokaryotes, making them more difficult to reliably recognize. Two classic examples of signals identified by eukaryotic gene finders are <a href="/wiki/CpG_island" class="mw-redirect" title="CpG island">CpG islands</a> and binding sites for a <a href="/wiki/Polyadenylation" title="Polyadenylation">poly(A) tail</a>. </p><p>Second, <a href="/wiki/RNA_splicing" title="RNA splicing">splicing</a> mechanisms employed by eukaryotic cells mean that a particular protein-coding sequence in the genome is divided into several parts (<a href="/wiki/Exons" class="mw-redirect" title="Exons">exons</a>), separated by non-coding sequences (<a href="/wiki/Introns" class="mw-redirect" title="Introns">introns</a>). (Splice sites are themselves another signal that eukaryotic gene finders are often designed to identify.) A typical protein-coding gene in humans might be divided into a dozen exons, each less than two hundred base pairs in length, and some as short as twenty to thirty. It is therefore much more difficult to detect periodicities and other known content properties of protein-coding DNA in eukaryotes. </p><p>Advanced gene finders for both prokaryotic and eukaryotic genomes typically use complex <a href="/wiki/Probabilistic_model" class="mw-redirect" title="Probabilistic model">probabilistic models</a>, such as <a href="/wiki/Hidden_Markov_model" title="Hidden Markov model">hidden Markov models</a> (HMMs) to combine information from a variety of different signal and content measurements. The <a href="/wiki/GLIMMER" title="GLIMMER">GLIMMER</a> system is a widely used and highly accurate gene finder for prokaryotes. <a href="/wiki/GeneMark" title="GeneMark">GeneMark</a> is another popular approach. Eukaryotic <i>ab initio</i> gene finders, by comparison, have achieved only limited success; notable examples are the <a href="/wiki/GENSCAN" title="GENSCAN">GENSCAN</a> and <a href="/w/index.php?title=Geneid&action=edit&redlink=1" class="new" title="Geneid (page does not exist)">geneid</a> programs. The GeneMark-ES and SNAP gene finders are GHMM-based like GENSCAN. They attempt to address problems related to using a gene finder on a genome sequence that it was not trained against.<sup id="cite_ref-7" class="reference"><a href="#cite_note-7"><span class="cite-bracket">[</span>7<span class="cite-bracket">]</span></a></sup> <sup id="cite_ref-8" class="reference"><a href="#cite_note-8"><span class="cite-bracket">[</span>8<span class="cite-bracket">]</span></a></sup> A few recent approaches like mSplicer,<sup id="cite_ref-9" class="reference"><a href="#cite_note-9"><span class="cite-bracket">[</span>9<span class="cite-bracket">]</span></a></sup> CONTRAST,<sup id="cite_ref-10" class="reference"><a href="#cite_note-10"><span class="cite-bracket">[</span>10<span class="cite-bracket">]</span></a></sup> or <a href="/w/index.php?title=MGene&action=edit&redlink=1" class="new" title="MGene (page does not exist)">mGene</a><sup id="cite_ref-11" class="reference"><a href="#cite_note-11"><span class="cite-bracket">[</span>11<span class="cite-bracket">]</span></a></sup> also use <a href="/wiki/Machine_learning" title="Machine learning">machine learning</a> techniques like <a href="/wiki/Support_vector_machines" class="mw-redirect" title="Support vector machines">support vector machines</a> for successful gene prediction. They build a <a href="/wiki/Discriminative_model" title="Discriminative model">discriminative model</a> using <a href="/w/index.php?title=Hidden_Markov_support_vector_machine&action=edit&redlink=1" class="new" title="Hidden Markov support vector machine (page does not exist)">hidden Markov support vector machines</a> or <a href="/wiki/Conditional_random_field" title="Conditional random field">conditional random fields</a> to learn an accurate gene prediction scoring function. </p><p><i>Ab Initio</i> methods have been benchmarked, with some approaching 100% sensitivity,<sup id="cite_ref-Yandell2012_3-1" class="reference"><a href="#cite_note-Yandell2012-3"><span class="cite-bracket">[</span>3<span class="cite-bracket">]</span></a></sup> however as the sensitivity increases, accuracy suffers as a result of increased <a href="/wiki/Type_I_and_type_II_errors#False_positive_error" title="Type I and type II errors">false positives</a>. </p> <div class="mw-heading mw-heading3"><h3 id="Other_signals">Other signals</h3><span class="mw-editsection"><span class="mw-editsection-bracket">[</span><a href="/w/index.php?title=Gene_prediction&action=edit&section=3" title="Edit section: Other signals"><span>edit</span></a><span class="mw-editsection-bracket">]</span></span></div> <p>Among the derived signals used for prediction are statistics resulting from the sub-sequence statistics like <a href="/wiki/K-mer" title="K-mer">k-mer</a> statistics, <a href="/wiki/Isochore_(genetics)" title="Isochore (genetics)">Isochore (genetics)</a> or <a href="/wiki/Compositional_domain" title="Compositional domain">Compositional domain</a> GC composition/uniformity/entropy, sequence and frame length, Intron/Exon/Donor/Acceptor/Promoter and <a href="/wiki/Ribosomal_binding_site" class="mw-redirect" title="Ribosomal binding site">Ribosomal binding site</a> vocabulary, <a href="/wiki/Fractal_dimension" title="Fractal dimension">Fractal dimension</a>, <a href="/wiki/Fourier_transform" title="Fourier transform">Fourier transform</a> of a pseudo-number-coded DNA, <a href="/wiki/Z-curve" class="mw-redirect" title="Z-curve">Z-curve</a> parameters and certain run features.<sup id="cite_ref-Saeys2007_12-0" class="reference"><a href="#cite_note-Saeys2007-12"><span class="cite-bracket">[</span>12<span class="cite-bracket">]</span></a></sup> </p><p>It has been suggested that signals other than those directly detectable in sequences may improve gene prediction. For example, the role of <a href="/wiki/Secondary_structure" class="mw-redirect" title="Secondary structure">secondary structure</a> in the identification of regulatory motifs has been reported.<sup id="cite_ref-Hiller2006_13-0" class="reference"><a href="#cite_note-Hiller2006-13"><span class="cite-bracket">[</span>13<span class="cite-bracket">]</span></a></sup> In addition, it has been suggested that RNA secondary structure prediction helps splice site prediction.<sup id="cite_ref-Patterson2002_14-0" class="reference"><a href="#cite_note-Patterson2002-14"><span class="cite-bracket">[</span>14<span class="cite-bracket">]</span></a></sup><sup id="cite_ref-Marashi2006a_15-0" class="reference"><a href="#cite_note-Marashi2006a-15"><span class="cite-bracket">[</span>15<span class="cite-bracket">]</span></a></sup><sup id="cite_ref-Marashi2006b_16-0" class="reference"><a href="#cite_note-Marashi2006b-16"><span class="cite-bracket">[</span>16<span class="cite-bracket">]</span></a></sup><sup id="cite_ref-Rogic2006_17-0" class="reference"><a href="#cite_note-Rogic2006-17"><span class="cite-bracket">[</span>17<span class="cite-bracket">]</span></a></sup> </p> <div class="mw-heading mw-heading3"><h3 id="Neural_networks">Neural networks</h3><span class="mw-editsection"><span class="mw-editsection-bracket">[</span><a href="/w/index.php?title=Gene_prediction&action=edit&section=4" title="Edit section: Neural networks"><span>edit</span></a><span class="mw-editsection-bracket">]</span></span></div> <p><a href="/wiki/Artificial_neural_networks" class="mw-redirect" title="Artificial neural networks">Artificial neural networks</a> are computational models that excel at <a href="/wiki/Machine_learning" title="Machine learning">machine learning</a> and <a href="/wiki/Pattern_recognition" title="Pattern recognition">pattern recognition</a>. Neural networks must be <a href="/wiki/Artificial_neural_network#Learning" class="mw-redirect" title="Artificial neural network">trained</a> with example data before being able to generalise for experimental data, and tested against benchmark data. Neural networks are able to come up with approximate solutions to problems that are hard to solve algorithmically, provided there is sufficient training data. When applied to gene prediction, neural networks can be used alongside other <i>ab initio</i> methods to predict or identify biological features such as splice sites.<sup id="cite_ref-Goel2013_18-0" class="reference"><a href="#cite_note-Goel2013-18"><span class="cite-bracket">[</span>18<span class="cite-bracket">]</span></a></sup> One approach<sup id="cite_ref-Johansen2009_19-0" class="reference"><a href="#cite_note-Johansen2009-19"><span class="cite-bracket">[</span>19<span class="cite-bracket">]</span></a></sup> involves using a sliding window, which traverses the sequence data in an overlapping manner. The output at each position is a score based on whether the network thinks the window contains a donor splice site or an acceptor splice site. Larger windows offer more accuracy but also require more computational power. A neural network is an example of a signal sensor as its goal is to identify a functional site in the genome. </p> <div class="mw-heading mw-heading2"><h2 id="Combined_approaches">Combined approaches</h2><span class="mw-editsection"><span class="mw-editsection-bracket">[</span><a href="/w/index.php?title=Gene_prediction&action=edit&section=5" title="Edit section: Combined approaches"><span>edit</span></a><span class="mw-editsection-bracket">]</span></span></div> <p>Programs such as Maker combine extrinsic and <i>ab initio</i> approaches by mapping protein and <a href="/wiki/Expressed_sequence_tag" title="Expressed sequence tag">EST</a> data to the genome to validate <i>ab initio</i> predictions. Augustus, which may be used as part of the Maker pipeline, can also incorporate hints in the form of EST alignments or protein profiles to increase the accuracy of the gene prediction. </p> <div class="mw-heading mw-heading2"><h2 id="Comparative_genomics_approaches">Comparative genomics approaches</h2><span class="mw-editsection"><span class="mw-editsection-bracket">[</span><a href="/w/index.php?title=Gene_prediction&action=edit&section=6" title="Edit section: Comparative genomics approaches"><span>edit</span></a><span class="mw-editsection-bracket">]</span></span></div> <p>As the entire genomes of many different species are sequenced, a promising direction in current research on gene finding is a <a href="/wiki/Comparative_genomics" title="Comparative genomics">comparative genomics</a> approach. </p><p>This is based on the principle that the forces of <a href="/wiki/Natural_selection" title="Natural selection">natural selection</a> cause genes and other functional elements to undergo mutation at a slower rate than the rest of the genome, since mutations in functional elements are more likely to negatively impact the organism than mutations elsewhere. Genes can thus be detected by comparing the genomes of related species to detect this evolutionary pressure for conservation. This approach was first applied to the mouse and human genomes, using programs such as SLAM, SGP and TWINSCAN/N-SCAN and CONTRAST.<sup id="cite_ref-:0_20-0" class="reference"><a href="#cite_note-:0-20"><span class="cite-bracket">[</span>20<span class="cite-bracket">]</span></a></sup> </p> <div class="mw-heading mw-heading3"><h3 id="Multiple_informants">Multiple informants</h3><span class="mw-editsection"><span class="mw-editsection-bracket">[</span><a href="/w/index.php?title=Gene_prediction&action=edit&section=7" title="Edit section: Multiple informants"><span>edit</span></a><span class="mw-editsection-bracket">]</span></span></div> <p>TWINSCAN examined only human-mouse synteny to look for orthologous genes. Programs such as N-SCAN and CONTRAST allowed the incorporation of alignments from multiple organisms, or in the case of N-SCAN, a single alternate organism from the target. The use of multiple informants can lead to significant improvements in accuracy.<sup id="cite_ref-:0_20-1" class="reference"><a href="#cite_note-:0-20"><span class="cite-bracket">[</span>20<span class="cite-bracket">]</span></a></sup> </p><p>CONTRAST is composed of two elements. The first is a smaller classifier, identifying donor splice sites and acceptor splice sites as well as start and stop codons. The second element involves constructing a full model using machine learning. Breaking the problem into two means that smaller targeted data sets can be used to train the classifiers, and that classifier can operate independently and be trained with smaller windows. The full model can use the independent classifier, and not have to waste computational time or model complexity re-classifying intron-exon boundaries. The paper in which CONTRAST is introduced proposes that their method (and those of TWINSCAN, etc.) be classified as <i>de novo</i> gene assembly, using alternate genomes, and identifying it as distinct from <i>ab initio</i>, which uses a target 'informant' genomes.<sup id="cite_ref-:0_20-2" class="reference"><a href="#cite_note-:0-20"><span class="cite-bracket">[</span>20<span class="cite-bracket">]</span></a></sup> </p><p>Comparative gene finding can also be used to project high quality annotations from one genome to another. Notable examples include Projector, GeneWise, GeneMapper and GeMoMa. Such techniques now play a central role in the annotation of all genomes. </p> <div class="mw-heading mw-heading2"><h2 id="Pseudogene_prediction">Pseudogene prediction</h2><span class="mw-editsection"><span class="mw-editsection-bracket">[</span><a href="/w/index.php?title=Gene_prediction&action=edit&section=8" title="Edit section: Pseudogene prediction"><span>edit</span></a><span class="mw-editsection-bracket">]</span></span></div> <p><a href="/wiki/Pseudogenes" class="mw-redirect" title="Pseudogenes">Pseudogenes</a> are close relatives of genes, sharing very high sequence homology, but being unable to code for the same <a href="/wiki/Protein" title="Protein">protein</a> product. Whilst once relegated as byproducts of <a href="/wiki/DNA_sequencing" title="DNA sequencing">gene sequencing</a>, increasingly, as regulatory roles are being uncovered, they are becoming predictive targets in their own right.<sup id="cite_ref-Alexander2010_21-0" class="reference"><a href="#cite_note-Alexander2010-21"><span class="cite-bracket">[</span>21<span class="cite-bracket">]</span></a></sup> Pseudogene prediction utilises existing sequence similarity and ab initio methods, whilst adding additional filtering and methods of identifying pseudogene characteristics. </p><p>Sequence similarity methods can be customised for pseudogene prediction using additional filtering to find candidate pseudogenes. This could use disablement detection, which looks for nonsense or frameshift mutations that would truncate or collapse an otherwise functional coding sequence.<sup id="cite_ref-Svensson2006_22-0" class="reference"><a href="#cite_note-Svensson2006-22"><span class="cite-bracket">[</span>22<span class="cite-bracket">]</span></a></sup> Additionally, translating DNA into proteins sequences can be more effective than just straight DNA homology.<sup id="cite_ref-Alexander2010_21-1" class="reference"><a href="#cite_note-Alexander2010-21"><span class="cite-bracket">[</span>21<span class="cite-bracket">]</span></a></sup> </p><p>Content sensors can be filtered according to the differences in statistical properties between pseudogenes and genes, such as a reduced count of CpG islands in pseudogenes, or the differences in G-C content between pseudogenes and their neighbours. Signal sensors also can be honed to pseudogenes, looking for the absence of introns or polyadenine tails. <sup id="cite_ref-Zhang2004_23-0" class="reference"><a href="#cite_note-Zhang2004-23"><span class="cite-bracket">[</span>23<span class="cite-bracket">]</span></a></sup> </p> <div class="mw-heading mw-heading2"><h2 id="Metagenomic_gene_prediction">Metagenomic gene prediction</h2><span class="mw-editsection"><span class="mw-editsection-bracket">[</span><a href="/w/index.php?title=Gene_prediction&action=edit&section=9" title="Edit section: Metagenomic gene prediction"><span>edit</span></a><span class="mw-editsection-bracket">]</span></span></div> <p><a href="/wiki/Metagenomics" title="Metagenomics">Metagenomics</a> is the study of genetic material recovered from the environment, resulting in sequence information from a pool of organisms. Predicting genes is useful for <a href="/wiki/Metagenomics#Comparative_metagenomics" title="Metagenomics">comparative metagenomics</a>. </p><p>Metagenomics tools also fall into the basic categories of using either sequence similarity approaches (MEGAN4) and ab initio techniques (GLIMMER-MG). </p><p>Glimmer-MG<sup id="cite_ref-Kelley2012_24-0" class="reference"><a href="#cite_note-Kelley2012-24"><span class="cite-bracket">[</span>24<span class="cite-bracket">]</span></a></sup> is an extension to <a href="/wiki/GLIMMER" title="GLIMMER">GLIMMER</a> that relies mostly on an ab initio approach for gene finding and by using training sets from related organisms. The prediction strategy is augmented by classification and clustering gene data sets prior to applying ab initio gene prediction methods. The data is clustered by species. This classification method leverages techniques from metagenomic phylogenetic classification. An example of software for this purpose is, Phymm, which uses interpolated markov models—and PhymmBL, which integrates BLAST into the classification routines. </p><p>MEGAN4<sup id="cite_ref-Huson2011_25-0" class="reference"><a href="#cite_note-Huson2011-25"><span class="cite-bracket">[</span>25<span class="cite-bracket">]</span></a></sup> uses a sequence similarity approach, using local alignment against databases of known sequences, but also attempts to classify using additional information on functional roles, biological pathways and enzymes. As in single organism gene prediction, sequence similarity approaches are limited by the size of the database. </p><p>FragGeneScan and MetaGeneAnnotator are popular gene prediction programs based on <a href="/wiki/Hidden_Markov_model" title="Hidden Markov model">Hidden Markov model</a>. These predictors account for sequencing errors, partial genes and work for short reads. </p><p>Another fast and accurate tool for gene prediction in metagenomes is MetaGeneMark.<sup id="cite_ref-Zhu2010_26-0" class="reference"><a href="#cite_note-Zhu2010-26"><span class="cite-bracket">[</span>26<span class="cite-bracket">]</span></a></sup> This tool is used by the DOE Joint Genome Institute to annotate IMG/M, the largest metagenome collection to date. </p> <div class="mw-heading mw-heading2"><h2 id="See_also">See also</h2><span class="mw-editsection"><span class="mw-editsection-bracket">[</span><a href="/w/index.php?title=Gene_prediction&action=edit&section=10" title="Edit section: See also"><span>edit</span></a><span class="mw-editsection-bracket">]</span></span></div> <ul><li><a href="/wiki/List_of_gene_prediction_software" title="List of gene prediction software">List of gene prediction software</a></li> <li><a href="/wiki/Phylogenetic_footprinting" title="Phylogenetic footprinting">Phylogenetic footprinting</a></li> <li><a href="/wiki/Protein_function_prediction" title="Protein function prediction">Protein function prediction</a></li> <li><a href="/wiki/Protein_structure_prediction" title="Protein structure prediction">Protein structure prediction</a></li> <li><a href="/wiki/Protein%E2%80%93protein_interaction_prediction" title="Protein–protein interaction prediction">Protein–protein interaction prediction</a></li> <li><a href="/wiki/Pseudogene_(database)" title="Pseudogene (database)">Pseudogene (database)</a></li> <li><a href="/wiki/Sequence_mining" class="mw-redirect" title="Sequence mining">Sequence mining</a></li> <li><a href="/wiki/Homology_(biology)" title="Homology (biology)">Sequence similarity (homology)</a></li></ul> <div class="mw-heading mw-heading2"><h2 id="References">References</h2><span class="mw-editsection"><span class="mw-editsection-bracket">[</span><a href="/w/index.php?title=Gene_prediction&action=edit&section=11" title="Edit section: References"><span>edit</span></a><span class="mw-editsection-bracket">]</span></span></div> <style data-mw-deduplicate="TemplateStyles:r1239543626">.mw-parser-output .reflist{margin-bottom:0.5em;list-style-type:decimal}@media screen{.mw-parser-output .reflist{font-size:90%}}.mw-parser-output .reflist .references{font-size:100%;margin-bottom:0;list-style-type:inherit}.mw-parser-output .reflist-columns-2{column-width:30em}.mw-parser-output .reflist-columns-3{column-width:25em}.mw-parser-output .reflist-columns{margin-top:0.3em}.mw-parser-output .reflist-columns ol{margin-top:0}.mw-parser-output .reflist-columns li{page-break-inside:avoid;break-inside:avoid-column}.mw-parser-output .reflist-upper-alpha{list-style-type:upper-alpha}.mw-parser-output .reflist-upper-roman{list-style-type:upper-roman}.mw-parser-output .reflist-lower-alpha{list-style-type:lower-alpha}.mw-parser-output .reflist-lower-greek{list-style-type:lower-greek}.mw-parser-output .reflist-lower-roman{list-style-type:lower-roman}</style><div class="reflist"> <div class="mw-references-wrap mw-references-columns"><ol class="references"> <li id="cite_note-Sleator2010-1"><span class="mw-cite-backlink"><b><a href="#cite_ref-Sleator2010_1-0">^</a></b></span> <span class="reference-text"><style data-mw-deduplicate="TemplateStyles:r1238218222">.mw-parser-output cite.citation{font-style:inherit;word-wrap:break-word}.mw-parser-output .citation q{quotes:"\"""\"""'""'"}.mw-parser-output .citation:target{background-color:rgba(0,127,255,0.133)}.mw-parser-output .id-lock-free.id-lock-free a{background:url("//upload.wikimedia.org/wikipedia/commons/6/65/Lock-green.svg")right 0.1em center/9px no-repeat}.mw-parser-output .id-lock-limited.id-lock-limited a,.mw-parser-output .id-lock-registration.id-lock-registration a{background:url("//upload.wikimedia.org/wikipedia/commons/d/d6/Lock-gray-alt-2.svg")right 0.1em center/9px no-repeat}.mw-parser-output .id-lock-subscription.id-lock-subscription a{background:url("//upload.wikimedia.org/wikipedia/commons/a/aa/Lock-red-alt-2.svg")right 0.1em center/9px no-repeat}.mw-parser-output .cs1-ws-icon a{background:url("//upload.wikimedia.org/wikipedia/commons/4/4c/Wikisource-logo.svg")right 0.1em center/12px no-repeat}body:not(.skin-timeless):not(.skin-minerva) .mw-parser-output .id-lock-free a,body:not(.skin-timeless):not(.skin-minerva) .mw-parser-output .id-lock-limited a,body:not(.skin-timeless):not(.skin-minerva) .mw-parser-output .id-lock-registration a,body:not(.skin-timeless):not(.skin-minerva) .mw-parser-output .id-lock-subscription a,body:not(.skin-timeless):not(.skin-minerva) .mw-parser-output .cs1-ws-icon a{background-size:contain;padding:0 1em 0 0}.mw-parser-output .cs1-code{color:inherit;background:inherit;border:none;padding:inherit}.mw-parser-output .cs1-hidden-error{display:none;color:var(--color-error,#d33)}.mw-parser-output .cs1-visible-error{color:var(--color-error,#d33)}.mw-parser-output .cs1-maint{display:none;color:#085;margin-left:0.3em}.mw-parser-output .cs1-kern-left{padding-left:0.2em}.mw-parser-output .cs1-kern-right{padding-right:0.2em}.mw-parser-output .citation .mw-selflink{font-weight:inherit}@media screen{.mw-parser-output .cs1-format{font-size:95%}html.skin-theme-clientpref-night .mw-parser-output .cs1-maint{color:#18911f}}@media screen and (prefers-color-scheme:dark){html.skin-theme-clientpref-os .mw-parser-output .cs1-maint{color:#18911f}}</style><cite id="CITEREFSleator2010" class="citation journal cs1">Sleator RD (August 2010). "An overview of the current status of eukaryote gene prediction strategies". <i>Gene</i>. <b>461</b> (1–2): 1–4. <a href="/wiki/Doi_(identifier)" class="mw-redirect" title="Doi (identifier)">doi</a>:<a rel="nofollow" class="external text" href="https://doi.org/10.1016%2Fj.gene.2010.04.008">10.1016/j.gene.2010.04.008</a>. <a href="/wiki/PMID_(identifier)" class="mw-redirect" title="PMID (identifier)">PMID</a> <a rel="nofollow" class="external text" href="https://pubmed.ncbi.nlm.nih.gov/20430068">20430068</a>.</cite><span title="ctx_ver=Z39.88-2004&rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&rft.genre=article&rft.jtitle=Gene&rft.atitle=An+overview+of+the+current+status+of+eukaryote+gene+prediction+strategies&rft.volume=461&rft.issue=1%E2%80%932&rft.pages=1-4&rft.date=2010-08&rft_id=info%3Adoi%2F10.1016%2Fj.gene.2010.04.008&rft_id=info%3Apmid%2F20430068&rft.aulast=Sleator&rft.aufirst=RD&rfr_id=info%3Asid%2Fen.wikipedia.org%3AGene+prediction" class="Z3988"></span></span> </li> <li id="cite_note-2"><span class="mw-cite-backlink"><b><a href="#cite_ref-2">^</a></b></span> <span class="reference-text"><link rel="mw-deduplicated-inline-style" href="mw-data:TemplateStyles:r1238218222"><cite id="CITEREFEjiguJung2020" class="citation journal cs1">Ejigu, Girum Fitihamlak; Jung, Jaehee (2020-09-18). <a rel="nofollow" class="external text" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7565776">"Review on the Computational Genome Annotation of Sequences Obtained by Next-Generation Sequencing"</a>. <i>Biology</i>. <b>9</b> (9): 295. <a href="/wiki/Doi_(identifier)" class="mw-redirect" title="Doi (identifier)">doi</a>:<span class="id-lock-free" title="Freely accessible"><a rel="nofollow" class="external text" href="https://doi.org/10.3390%2Fbiology9090295">10.3390/biology9090295</a></span>. <a href="/wiki/ISSN_(identifier)" class="mw-redirect" title="ISSN (identifier)">ISSN</a> <a rel="nofollow" class="external text" href="https://search.worldcat.org/issn/2079-7737">2079-7737</a>. <a href="/wiki/PMC_(identifier)" class="mw-redirect" title="PMC (identifier)">PMC</a> <span class="id-lock-free" title="Freely accessible"><a rel="nofollow" class="external text" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7565776">7565776</a></span>. <a href="/wiki/PMID_(identifier)" class="mw-redirect" title="PMID (identifier)">PMID</a> <a rel="nofollow" class="external text" href="https://pubmed.ncbi.nlm.nih.gov/32962098">32962098</a>.</cite><span title="ctx_ver=Z39.88-2004&rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&rft.genre=article&rft.jtitle=Biology&rft.atitle=Review+on+the+Computational+Genome+Annotation+of+Sequences+Obtained+by+Next-Generation+Sequencing&rft.volume=9&rft.issue=9&rft.pages=295&rft.date=2020-09-18&rft_id=https%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fpmc%2Farticles%2FPMC7565776%23id-name%3DPMC&rft.issn=2079-7737&rft_id=info%3Apmid%2F32962098&rft_id=info%3Adoi%2F10.3390%2Fbiology9090295&rft.aulast=Ejigu&rft.aufirst=Girum+Fitihamlak&rft.au=Jung%2C+Jaehee&rft_id=https%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fpmc%2Farticles%2FPMC7565776&rfr_id=info%3Asid%2Fen.wikipedia.org%3AGene+prediction" class="Z3988"></span></span> </li> <li id="cite_note-Yandell2012-3"><span class="mw-cite-backlink">^ <a href="#cite_ref-Yandell2012_3-0"><sup><i><b>a</b></i></sup></a> <a href="#cite_ref-Yandell2012_3-1"><sup><i><b>b</b></i></sup></a></span> <span class="reference-text"><link rel="mw-deduplicated-inline-style" href="mw-data:TemplateStyles:r1238218222"><cite id="CITEREFYandellEnce2012" class="citation journal cs1">Yandell M, Ence D (April 2012). "A beginner's guide to eukaryotic genome annotation". <i>Nature Reviews. Genetics</i>. <b>13</b> (5): 329–42. <a href="/wiki/Doi_(identifier)" class="mw-redirect" title="Doi (identifier)">doi</a>:<a rel="nofollow" class="external text" href="https://doi.org/10.1038%2Fnrg3174">10.1038/nrg3174</a>. <a href="/wiki/PMID_(identifier)" class="mw-redirect" title="PMID (identifier)">PMID</a> <a rel="nofollow" class="external text" href="https://pubmed.ncbi.nlm.nih.gov/22510764">22510764</a>. <a href="/wiki/S2CID_(identifier)" class="mw-redirect" title="S2CID (identifier)">S2CID</a> <a rel="nofollow" class="external text" href="https://api.semanticscholar.org/CorpusID:3352427">3352427</a>.</cite><span title="ctx_ver=Z39.88-2004&rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&rft.genre=article&rft.jtitle=Nature+Reviews.+Genetics&rft.atitle=A+beginner%27s+guide+to+eukaryotic+genome+annotation&rft.volume=13&rft.issue=5&rft.pages=329-42&rft.date=2012-04&rft_id=https%3A%2F%2Fapi.semanticscholar.org%2FCorpusID%3A3352427%23id-name%3DS2CID&rft_id=info%3Apmid%2F22510764&rft_id=info%3Adoi%2F10.1038%2Fnrg3174&rft.aulast=Yandell&rft.aufirst=M&rft.au=Ence%2C+D&rfr_id=info%3Asid%2Fen.wikipedia.org%3AGene+prediction" class="Z3988"></span></span> </li> <li id="cite_note-redding2013-4"><span class="mw-cite-backlink"><b><a href="#cite_ref-redding2013_4-0">^</a></b></span> <span class="reference-text"><link rel="mw-deduplicated-inline-style" href="mw-data:TemplateStyles:r1238218222"><cite id="CITEREFReddingGreene2013" class="citation journal cs1">Redding S, Greene EC (May 2013). <a rel="nofollow" class="external text" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3810971">"How do proteins locate specific targets in DNA?"</a>. <i>Chemical Physics Letters</i>. <b>570</b>: 1–11. <a href="/wiki/Bibcode_(identifier)" class="mw-redirect" title="Bibcode (identifier)">Bibcode</a>:<a rel="nofollow" class="external text" href="https://ui.adsabs.harvard.edu/abs/2013CPL...570....1R">2013CPL...570....1R</a>. <a href="/wiki/Doi_(identifier)" class="mw-redirect" title="Doi (identifier)">doi</a>:<a rel="nofollow" class="external text" href="https://doi.org/10.1016%2Fj.cplett.2013.03.035">10.1016/j.cplett.2013.03.035</a>. <a href="/wiki/PMC_(identifier)" class="mw-redirect" title="PMC (identifier)">PMC</a> <span class="id-lock-free" title="Freely accessible"><a rel="nofollow" class="external text" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3810971">3810971</a></span>. <a href="/wiki/PMID_(identifier)" class="mw-redirect" title="PMID (identifier)">PMID</a> <a rel="nofollow" class="external text" href="https://pubmed.ncbi.nlm.nih.gov/24187380">24187380</a>.</cite><span title="ctx_ver=Z39.88-2004&rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&rft.genre=article&rft.jtitle=Chemical+Physics+Letters&rft.atitle=How+do+proteins+locate+specific+targets+in+DNA%3F&rft.volume=570&rft.pages=1-11&rft.date=2013-05&rft_id=https%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fpmc%2Farticles%2FPMC3810971%23id-name%3DPMC&rft_id=info%3Apmid%2F24187380&rft_id=info%3Adoi%2F10.1016%2Fj.cplett.2013.03.035&rft_id=info%3Abibcode%2F2013CPL...570....1R&rft.aulast=Redding&rft.aufirst=S&rft.au=Greene%2C+EC&rft_id=https%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fpmc%2Farticles%2FPMC3810971&rfr_id=info%3Asid%2Fen.wikipedia.org%3AGene+prediction" class="Z3988"></span></span> </li> <li id="cite_note-sokolov2005-5"><span class="mw-cite-backlink"><b><a href="#cite_ref-sokolov2005_5-0">^</a></b></span> <span class="reference-text"><link rel="mw-deduplicated-inline-style" href="mw-data:TemplateStyles:r1238218222"><cite id="CITEREFSokolovMetzlerPantWilliams2005" class="citation journal cs1">Sokolov IM, Metzler R, Pant K, Williams MC (August 2005). <a rel="nofollow" class="external text" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1366639">"Target search of N sliding proteins on a DNA"</a>. <i>Biophysical Journal</i>. <b>89</b> (2): 895–902. <a href="/wiki/Bibcode_(identifier)" class="mw-redirect" title="Bibcode (identifier)">Bibcode</a>:<a rel="nofollow" class="external text" href="https://ui.adsabs.harvard.edu/abs/2005BpJ....89..895S">2005BpJ....89..895S</a>. <a href="/wiki/Doi_(identifier)" class="mw-redirect" title="Doi (identifier)">doi</a>:<a rel="nofollow" class="external text" href="https://doi.org/10.1529%2Fbiophysj.104.057612">10.1529/biophysj.104.057612</a>. <a href="/wiki/PMC_(identifier)" class="mw-redirect" title="PMC (identifier)">PMC</a> <span class="id-lock-free" title="Freely accessible"><a rel="nofollow" class="external text" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1366639">1366639</a></span>. <a href="/wiki/PMID_(identifier)" class="mw-redirect" title="PMID (identifier)">PMID</a> <a rel="nofollow" class="external text" href="https://pubmed.ncbi.nlm.nih.gov/15908574">15908574</a>.</cite><span title="ctx_ver=Z39.88-2004&rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&rft.genre=article&rft.jtitle=Biophysical+Journal&rft.atitle=Target+search+of+N+sliding+proteins+on+a+DNA&rft.volume=89&rft.issue=2&rft.pages=895-902&rft.date=2005-08&rft_id=https%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fpmc%2Farticles%2FPMC1366639%23id-name%3DPMC&rft_id=info%3Apmid%2F15908574&rft_id=info%3Adoi%2F10.1529%2Fbiophysj.104.057612&rft_id=info%3Abibcode%2F2005BpJ....89..895S&rft.aulast=Sokolov&rft.aufirst=IM&rft.au=Metzler%2C+R&rft.au=Pant%2C+K&rft.au=Williams%2C+MC&rft_id=https%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fpmc%2Farticles%2FPMC1366639&rfr_id=info%3Asid%2Fen.wikipedia.org%3AGene+prediction" class="Z3988"></span></span> </li> <li id="cite_note-6"><span class="mw-cite-backlink"><b><a href="#cite_ref-6">^</a></b></span> <span class="reference-text"><link rel="mw-deduplicated-inline-style" href="mw-data:TemplateStyles:r1238218222"><cite id="CITEREFMadiganMartinkoBenderBuckley2015" class="citation book cs1">Madigan MT, Martinko JM, Bender KS, Buckley DH, Stahl D (2015). <i>Brock Biology of Microorganisms</i> (14th ed.). Boston: Pearson. <a href="/wiki/ISBN_(identifier)" class="mw-redirect" title="ISBN (identifier)">ISBN</a> <a href="/wiki/Special:BookSources/9780321897398" title="Special:BookSources/9780321897398"><bdi>9780321897398</bdi></a>.</cite><span title="ctx_ver=Z39.88-2004&rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Abook&rft.genre=book&rft.btitle=Brock+Biology+of+Microorganisms&rft.place=Boston&rft.edition=14th&rft.pub=Pearson&rft.date=2015&rft.isbn=9780321897398&rft.aulast=Madigan&rft.aufirst=Michael+T.&rft.au=Martinko%2C+John+M.&rft.au=Bender%2C+Kelly+S.&rft.au=Buckley%2C+Daniel+H.&rft.au=Stahl%2C+David&rfr_id=info%3Asid%2Fen.wikipedia.org%3AGene+prediction" class="Z3988"></span></span> </li> <li id="cite_note-7"><span class="mw-cite-backlink"><b><a href="#cite_ref-7">^</a></b></span> <span class="reference-text"><link rel="mw-deduplicated-inline-style" href="mw-data:TemplateStyles:r1238218222"><cite class="citation web cs1"><a rel="nofollow" class="external text" href="https://academic.oup.com/nar/article/33/20/6494/1082033">"GeneMark-ES"</a>.</cite><span title="ctx_ver=Z39.88-2004&rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Abook&rft.genre=unknown&rft.btitle=GeneMark-ES&rft_id=https%3A%2F%2Facademic.oup.com%2Fnar%2Farticle%2F33%2F20%2F6494%2F1082033&rfr_id=info%3Asid%2Fen.wikipedia.org%3AGene+prediction" class="Z3988"></span></span> </li> <li id="cite_note-8"><span class="mw-cite-backlink"><b><a href="#cite_ref-8">^</a></b></span> <span class="reference-text"><link rel="mw-deduplicated-inline-style" href="mw-data:TemplateStyles:r1238218222"><cite id="CITEREFKorf2004" class="citation journal cs1">Korf I (May 2004). <a rel="nofollow" class="external text" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC421630">"Gene finding in novel genomes"</a>. <i>BMC Bioinformatics</i>. <b>5</b>: 59. <a href="/wiki/Doi_(identifier)" class="mw-redirect" title="Doi (identifier)">doi</a>:<span class="id-lock-free" title="Freely accessible"><a rel="nofollow" class="external text" href="https://doi.org/10.1186%2F1471-2105-5-59">10.1186/1471-2105-5-59</a></span>. <a href="/wiki/PMC_(identifier)" class="mw-redirect" title="PMC (identifier)">PMC</a> <span class="id-lock-free" title="Freely accessible"><a rel="nofollow" class="external text" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC421630">421630</a></span>. <a href="/wiki/PMID_(identifier)" class="mw-redirect" title="PMID (identifier)">PMID</a> <a rel="nofollow" class="external text" href="https://pubmed.ncbi.nlm.nih.gov/15144565">15144565</a>.</cite><span title="ctx_ver=Z39.88-2004&rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&rft.genre=article&rft.jtitle=BMC+Bioinformatics&rft.atitle=Gene+finding+in+novel+genomes&rft.volume=5&rft.pages=59&rft.date=2004-05&rft_id=https%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fpmc%2Farticles%2FPMC421630%23id-name%3DPMC&rft_id=info%3Apmid%2F15144565&rft_id=info%3Adoi%2F10.1186%2F1471-2105-5-59&rft.aulast=Korf&rft.aufirst=I&rft_id=https%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fpmc%2Farticles%2FPMC421630&rfr_id=info%3Asid%2Fen.wikipedia.org%3AGene+prediction" class="Z3988"></span></span> </li> <li id="cite_note-9"><span class="mw-cite-backlink"><b><a href="#cite_ref-9">^</a></b></span> <span class="reference-text"><link rel="mw-deduplicated-inline-style" href="mw-data:TemplateStyles:r1238218222"><cite id="CITEREFRätschSonnenburgSrinivasanWitte2007" class="citation journal cs1">Rätsch G, Sonnenburg S, Srinivasan J, Witte H, <a href="/wiki/Klaus-Robert_M%C3%BCller" title="Klaus-Robert Müller">Müller KR</a>, Sommer RJ, Schölkopf B (February 2007). <a rel="nofollow" class="external text" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1808025">"Improving the Caenorhabditis elegans genome annotation using machine learning"</a>. <i>PLOS Computational Biology</i>. <b>3</b> (2): e20. <a href="/wiki/Bibcode_(identifier)" class="mw-redirect" title="Bibcode (identifier)">Bibcode</a>:<a rel="nofollow" class="external text" href="https://ui.adsabs.harvard.edu/abs/2007PLSCB...3...20R">2007PLSCB...3...20R</a>. <a href="/wiki/Doi_(identifier)" class="mw-redirect" title="Doi (identifier)">doi</a>:<span class="id-lock-free" title="Freely accessible"><a rel="nofollow" class="external text" href="https://doi.org/10.1371%2Fjournal.pcbi.0030020">10.1371/journal.pcbi.0030020</a></span>. <a href="/wiki/PMC_(identifier)" class="mw-redirect" title="PMC (identifier)">PMC</a> <span class="id-lock-free" title="Freely accessible"><a rel="nofollow" class="external text" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1808025">1808025</a></span>. <a href="/wiki/PMID_(identifier)" class="mw-redirect" title="PMID (identifier)">PMID</a> <a rel="nofollow" class="external text" href="https://pubmed.ncbi.nlm.nih.gov/17319737">17319737</a>.</cite><span title="ctx_ver=Z39.88-2004&rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&rft.genre=article&rft.jtitle=PLOS+Computational+Biology&rft.atitle=Improving+the+Caenorhabditis+elegans+genome+annotation+using+machine+learning&rft.volume=3&rft.issue=2&rft.pages=e20&rft.date=2007-02&rft_id=https%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fpmc%2Farticles%2FPMC1808025%23id-name%3DPMC&rft_id=info%3Apmid%2F17319737&rft_id=info%3Adoi%2F10.1371%2Fjournal.pcbi.0030020&rft_id=info%3Abibcode%2F2007PLSCB...3...20R&rft.aulast=R%C3%A4tsch&rft.aufirst=G&rft.au=Sonnenburg%2C+S&rft.au=Srinivasan%2C+J&rft.au=Witte%2C+H&rft.au=M%C3%BCller%2C+KR&rft.au=Sommer%2C+RJ&rft.au=Sch%C3%B6lkopf%2C+B&rft_id=https%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fpmc%2Farticles%2FPMC1808025&rfr_id=info%3Asid%2Fen.wikipedia.org%3AGene+prediction" class="Z3988"></span></span> </li> <li id="cite_note-10"><span class="mw-cite-backlink"><b><a href="#cite_ref-10">^</a></b></span> <span class="reference-text"><link rel="mw-deduplicated-inline-style" href="mw-data:TemplateStyles:r1238218222"><cite id="CITEREFGrossDoSirotaBatzoglou2007" class="citation journal cs1">Gross SS, Do CB, Sirota M, Batzoglou S (2007-12-20). <a rel="nofollow" class="external text" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2246271">"CONTRAST: a discriminative, phylogeny-free approach to multiple informant de novo gene prediction"</a>. <i>Genome Biology</i>. <b>8</b> (12): R269. <a href="/wiki/Doi_(identifier)" class="mw-redirect" title="Doi (identifier)">doi</a>:<span class="id-lock-free" title="Freely accessible"><a rel="nofollow" class="external text" href="https://doi.org/10.1186%2Fgb-2007-8-12-r269">10.1186/gb-2007-8-12-r269</a></span>. <a href="/wiki/PMC_(identifier)" class="mw-redirect" title="PMC (identifier)">PMC</a> <span class="id-lock-free" title="Freely accessible"><a rel="nofollow" class="external text" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2246271">2246271</a></span>. <a href="/wiki/PMID_(identifier)" class="mw-redirect" title="PMID (identifier)">PMID</a> <a rel="nofollow" class="external text" href="https://pubmed.ncbi.nlm.nih.gov/18096039">18096039</a>.</cite><span title="ctx_ver=Z39.88-2004&rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&rft.genre=article&rft.jtitle=Genome+Biology&rft.atitle=CONTRAST%3A+a+discriminative%2C+phylogeny-free+approach+to+multiple+informant+de+novo+gene+prediction&rft.volume=8&rft.issue=12&rft.pages=R269&rft.date=2007-12-20&rft_id=https%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fpmc%2Farticles%2FPMC2246271%23id-name%3DPMC&rft_id=info%3Apmid%2F18096039&rft_id=info%3Adoi%2F10.1186%2Fgb-2007-8-12-r269&rft.aulast=Gross&rft.aufirst=SS&rft.au=Do%2C+CB&rft.au=Sirota%2C+M&rft.au=Batzoglou%2C+S&rft_id=https%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fpmc%2Farticles%2FPMC2246271&rfr_id=info%3Asid%2Fen.wikipedia.org%3AGene+prediction" class="Z3988"></span></span> </li> <li id="cite_note-11"><span class="mw-cite-backlink"><b><a href="#cite_ref-11">^</a></b></span> <span class="reference-text"><link rel="mw-deduplicated-inline-style" href="mw-data:TemplateStyles:r1238218222"><cite id="CITEREFSchweikertBehrZienZeller2009" class="citation journal cs1">Schweikert G, Behr J, Zien A, Zeller G, Ong CS, Sonnenburg S, Rätsch G (July 2009). <a rel="nofollow" class="external text" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2703990">"mGene.web: a web service for accurate computational gene finding"</a>. <i>Nucleic Acids Research</i>. <b>37</b> (Web Server issue): W312–6. <a href="/wiki/Doi_(identifier)" class="mw-redirect" title="Doi (identifier)">doi</a>:<a rel="nofollow" class="external text" href="https://doi.org/10.1093%2Fnar%2Fgkp479">10.1093/nar/gkp479</a>. <a href="/wiki/PMC_(identifier)" class="mw-redirect" title="PMC (identifier)">PMC</a> <span class="id-lock-free" title="Freely accessible"><a rel="nofollow" class="external text" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2703990">2703990</a></span>. <a href="/wiki/PMID_(identifier)" class="mw-redirect" title="PMID (identifier)">PMID</a> <a rel="nofollow" class="external text" href="https://pubmed.ncbi.nlm.nih.gov/19494180">19494180</a>.</cite><span title="ctx_ver=Z39.88-2004&rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&rft.genre=article&rft.jtitle=Nucleic+Acids+Research&rft.atitle=mGene.web%3A+a+web+service+for+accurate+computational+gene+finding&rft.volume=37&rft.issue=Web+Server+issue&rft.pages=W312-6&rft.date=2009-07&rft_id=https%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fpmc%2Farticles%2FPMC2703990%23id-name%3DPMC&rft_id=info%3Apmid%2F19494180&rft_id=info%3Adoi%2F10.1093%2Fnar%2Fgkp479&rft.aulast=Schweikert&rft.aufirst=G&rft.au=Behr%2C+J&rft.au=Zien%2C+A&rft.au=Zeller%2C+G&rft.au=Ong%2C+CS&rft.au=Sonnenburg%2C+S&rft.au=R%C3%A4tsch%2C+G&rft_id=https%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fpmc%2Farticles%2FPMC2703990&rfr_id=info%3Asid%2Fen.wikipedia.org%3AGene+prediction" class="Z3988"></span></span> </li> <li id="cite_note-Saeys2007-12"><span class="mw-cite-backlink"><b><a href="#cite_ref-Saeys2007_12-0">^</a></b></span> <span class="reference-text"><link rel="mw-deduplicated-inline-style" href="mw-data:TemplateStyles:r1238218222"><cite id="CITEREFSaeysRouzéVan_de_Peer2007" class="citation journal cs1">Saeys Y, Rouzé P, Van de Peer Y (February 2007). <a rel="nofollow" class="external text" href="https://doi.org/10.1093%2Fbioinformatics%2Fbtl639">"In search of the small ones: improved prediction of short exons in vertebrates, plants, fungi and protists"</a>. <i>Bioinformatics</i>. <b>23</b> (4): 414–20. <a href="/wiki/Doi_(identifier)" class="mw-redirect" title="Doi (identifier)">doi</a>:<span class="id-lock-free" title="Freely accessible"><a rel="nofollow" class="external text" href="https://doi.org/10.1093%2Fbioinformatics%2Fbtl639">10.1093/bioinformatics/btl639</a></span>. <a href="/wiki/PMID_(identifier)" class="mw-redirect" title="PMID (identifier)">PMID</a> <a rel="nofollow" class="external text" href="https://pubmed.ncbi.nlm.nih.gov/17204465">17204465</a>.</cite><span title="ctx_ver=Z39.88-2004&rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&rft.genre=article&rft.jtitle=Bioinformatics&rft.atitle=In+search+of+the+small+ones%3A+improved+prediction+of+short+exons+in+vertebrates%2C+plants%2C+fungi+and+protists&rft.volume=23&rft.issue=4&rft.pages=414-20&rft.date=2007-02&rft_id=info%3Adoi%2F10.1093%2Fbioinformatics%2Fbtl639&rft_id=info%3Apmid%2F17204465&rft.aulast=Saeys&rft.aufirst=Y&rft.au=Rouz%C3%A9%2C+P&rft.au=Van+de+Peer%2C+Y&rft_id=https%3A%2F%2Fdoi.org%2F10.1093%252Fbioinformatics%252Fbtl639&rfr_id=info%3Asid%2Fen.wikipedia.org%3AGene+prediction" class="Z3988"></span></span> </li> <li id="cite_note-Hiller2006-13"><span class="mw-cite-backlink"><b><a href="#cite_ref-Hiller2006_13-0">^</a></b></span> <span class="reference-text"><link rel="mw-deduplicated-inline-style" href="mw-data:TemplateStyles:r1238218222"><cite id="CITEREFHillerPudimatBuschBackofen2006" class="citation journal cs1">Hiller M, Pudimat R, Busch A, Backofen R (2006). <a rel="nofollow" class="external text" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1903381">"Using RNA secondary structures to guide sequence motif finding towards single-stranded regions"</a>. <i>Nucleic Acids Research</i>. <b>34</b> (17): e117. <a href="/wiki/Doi_(identifier)" class="mw-redirect" title="Doi (identifier)">doi</a>:<a rel="nofollow" class="external text" href="https://doi.org/10.1093%2Fnar%2Fgkl544">10.1093/nar/gkl544</a>. <a href="/wiki/PMC_(identifier)" class="mw-redirect" title="PMC (identifier)">PMC</a> <span class="id-lock-free" title="Freely accessible"><a rel="nofollow" class="external text" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1903381">1903381</a></span>. <a href="/wiki/PMID_(identifier)" class="mw-redirect" title="PMID (identifier)">PMID</a> <a rel="nofollow" class="external text" href="https://pubmed.ncbi.nlm.nih.gov/16987907">16987907</a>.</cite><span title="ctx_ver=Z39.88-2004&rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&rft.genre=article&rft.jtitle=Nucleic+Acids+Research&rft.atitle=Using+RNA+secondary+structures+to+guide+sequence+motif+finding+towards+single-stranded+regions&rft.volume=34&rft.issue=17&rft.pages=e117&rft.date=2006&rft_id=https%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fpmc%2Farticles%2FPMC1903381%23id-name%3DPMC&rft_id=info%3Apmid%2F16987907&rft_id=info%3Adoi%2F10.1093%2Fnar%2Fgkl544&rft.aulast=Hiller&rft.aufirst=M&rft.au=Pudimat%2C+R&rft.au=Busch%2C+A&rft.au=Backofen%2C+R&rft_id=https%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fpmc%2Farticles%2FPMC1903381&rfr_id=info%3Asid%2Fen.wikipedia.org%3AGene+prediction" class="Z3988"></span></span> </li> <li id="cite_note-Patterson2002-14"><span class="mw-cite-backlink"><b><a href="#cite_ref-Patterson2002_14-0">^</a></b></span> <span class="reference-text"><link rel="mw-deduplicated-inline-style" href="mw-data:TemplateStyles:r1238218222"><cite id="CITEREFPattersonYasuharaRuzzo2002" class="citation journal cs1">Patterson DJ, Yasuhara K, Ruzzo WL (2002). "Pre-mRNA secondary structure prediction aids splice site prediction". <i>Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing</i>: 223–34. <a href="/wiki/PMID_(identifier)" class="mw-redirect" title="PMID (identifier)">PMID</a> <a rel="nofollow" class="external text" href="https://pubmed.ncbi.nlm.nih.gov/11928478">11928478</a>.</cite><span title="ctx_ver=Z39.88-2004&rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&rft.genre=article&rft.jtitle=Pacific+Symposium+on+Biocomputing.+Pacific+Symposium+on+Biocomputing&rft.atitle=Pre-mRNA+secondary+structure+prediction+aids+splice+site+prediction&rft.pages=223-34&rft.date=2002&rft_id=info%3Apmid%2F11928478&rft.aulast=Patterson&rft.aufirst=DJ&rft.au=Yasuhara%2C+K&rft.au=Ruzzo%2C+WL&rfr_id=info%3Asid%2Fen.wikipedia.org%3AGene+prediction" class="Z3988"></span></span> </li> <li id="cite_note-Marashi2006a-15"><span class="mw-cite-backlink"><b><a href="#cite_ref-Marashi2006a_15-0">^</a></b></span> <span class="reference-text"><link rel="mw-deduplicated-inline-style" href="mw-data:TemplateStyles:r1238218222"><cite id="CITEREFMarashiGoodarziSadeghiEslahchi2006" class="citation journal cs1">Marashi SA, Goodarzi H, Sadeghi M, Eslahchi C, Pezeshk H (February 2006). "Importance of RNA secondary structure information for yeast donor and acceptor splice site predictions by neural networks". <i>Computational Biology and Chemistry</i>. <b>30</b> (1): 50–7. <a href="/wiki/Doi_(identifier)" class="mw-redirect" title="Doi (identifier)">doi</a>:<a rel="nofollow" class="external text" href="https://doi.org/10.1016%2Fj.compbiolchem.2005.10.009">10.1016/j.compbiolchem.2005.10.009</a>. <a href="/wiki/PMID_(identifier)" class="mw-redirect" title="PMID (identifier)">PMID</a> <a rel="nofollow" class="external text" href="https://pubmed.ncbi.nlm.nih.gov/16386465">16386465</a>.</cite><span title="ctx_ver=Z39.88-2004&rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&rft.genre=article&rft.jtitle=Computational+Biology+and+Chemistry&rft.atitle=Importance+of+RNA+secondary+structure+information+for+yeast+donor+and+acceptor+splice+site+predictions+by+neural+networks&rft.volume=30&rft.issue=1&rft.pages=50-7&rft.date=2006-02&rft_id=info%3Adoi%2F10.1016%2Fj.compbiolchem.2005.10.009&rft_id=info%3Apmid%2F16386465&rft.aulast=Marashi&rft.aufirst=SA&rft.au=Goodarzi%2C+H&rft.au=Sadeghi%2C+M&rft.au=Eslahchi%2C+C&rft.au=Pezeshk%2C+H&rfr_id=info%3Asid%2Fen.wikipedia.org%3AGene+prediction" class="Z3988"></span></span> </li> <li id="cite_note-Marashi2006b-16"><span class="mw-cite-backlink"><b><a href="#cite_ref-Marashi2006b_16-0">^</a></b></span> <span class="reference-text"><link rel="mw-deduplicated-inline-style" href="mw-data:TemplateStyles:r1238218222"><cite id="CITEREFMarashiEslahchiPezeshkSadeghi2006" class="citation journal cs1">Marashi SA, Eslahchi C, Pezeshk H, Sadeghi M (June 2006). <a rel="nofollow" class="external text" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1526458">"Impact of RNA structure on the prediction of donor and acceptor splice sites"</a>. <i>BMC Bioinformatics</i>. <b>7</b>: 297. <a href="/wiki/Doi_(identifier)" class="mw-redirect" title="Doi (identifier)">doi</a>:<span class="id-lock-free" title="Freely accessible"><a rel="nofollow" class="external text" href="https://doi.org/10.1186%2F1471-2105-7-297">10.1186/1471-2105-7-297</a></span>. <a href="/wiki/PMC_(identifier)" class="mw-redirect" title="PMC (identifier)">PMC</a> <span class="id-lock-free" title="Freely accessible"><a rel="nofollow" class="external text" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1526458">1526458</a></span>. <a href="/wiki/PMID_(identifier)" class="mw-redirect" title="PMID (identifier)">PMID</a> <a rel="nofollow" class="external text" href="https://pubmed.ncbi.nlm.nih.gov/16772025">16772025</a>.</cite><span title="ctx_ver=Z39.88-2004&rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&rft.genre=article&rft.jtitle=BMC+Bioinformatics&rft.atitle=Impact+of+RNA+structure+on+the+prediction+of+donor+and+acceptor+splice+sites&rft.volume=7&rft.pages=297&rft.date=2006-06&rft_id=https%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fpmc%2Farticles%2FPMC1526458%23id-name%3DPMC&rft_id=info%3Apmid%2F16772025&rft_id=info%3Adoi%2F10.1186%2F1471-2105-7-297&rft.aulast=Marashi&rft.aufirst=SA&rft.au=Eslahchi%2C+C&rft.au=Pezeshk%2C+H&rft.au=Sadeghi%2C+M&rft_id=https%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fpmc%2Farticles%2FPMC1526458&rfr_id=info%3Asid%2Fen.wikipedia.org%3AGene+prediction" class="Z3988"></span></span> </li> <li id="cite_note-Rogic2006-17"><span class="mw-cite-backlink"><b><a href="#cite_ref-Rogic2006_17-0">^</a></b></span> <span class="reference-text"><link rel="mw-deduplicated-inline-style" href="mw-data:TemplateStyles:r1238218222"><cite id="CITEREFRogic,_S2006" class="citation thesis cs1">Rogic, S (2006). <a rel="nofollow" class="external text" href="https://web.archive.org/web/20090530023145/http://www.cs.ubc.ca/grads/resources/thesis/Nov06/Rogic_Sanja.pdf"><i>The role of pre-mRNA secondary structure in gene splicing in </i>Saccharomyces cerevisiae<i><span></span></i></a> <span class="cs1-format">(PDF)</span> (PhD thesis). University of British Columbia. Archived from <a rel="nofollow" class="external text" href="http://www.cs.ubc.ca/grads/resources/thesis/Nov06/Rogic_Sanja.pdf">the original</a> <span class="cs1-format">(PDF)</span> on 2009-05-30<span class="reference-accessdate">. Retrieved <span class="nowrap">2007-04-01</span></span>.</cite><span title="ctx_ver=Z39.88-2004&rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Adissertation&rft.title=The+role+of+pre-mRNA+secondary+structure+in+gene+splicing+in+Saccharomyces+cerevisiae&rft.degree=PhD&rft.inst=University+of+British+Columbia&rft.date=2006&rft.au=Rogic%2C+S&rft_id=http%3A%2F%2Fwww.cs.ubc.ca%2Fgrads%2Fresources%2Fthesis%2FNov06%2FRogic_Sanja.pdf&rfr_id=info%3Asid%2Fen.wikipedia.org%3AGene+prediction" class="Z3988"></span></span> </li> <li id="cite_note-Goel2013-18"><span class="mw-cite-backlink"><b><a href="#cite_ref-Goel2013_18-0">^</a></b></span> <span class="reference-text"><link rel="mw-deduplicated-inline-style" href="mw-data:TemplateStyles:r1238218222"><cite id="CITEREFGoelSinghAseri2013" class="citation journal cs1">Goel N, Singh S, Aseri TC (July 2013). "A comparative analysis of soft computing techniques for gene prediction". <i>Analytical Biochemistry</i>. <b>438</b> (1): 14–21. <a href="/wiki/Doi_(identifier)" class="mw-redirect" title="Doi (identifier)">doi</a>:<a rel="nofollow" class="external text" href="https://doi.org/10.1016%2Fj.ab.2013.03.015">10.1016/j.ab.2013.03.015</a>. <a href="/wiki/PMID_(identifier)" class="mw-redirect" title="PMID (identifier)">PMID</a> <a rel="nofollow" class="external text" href="https://pubmed.ncbi.nlm.nih.gov/23529114">23529114</a>.</cite><span title="ctx_ver=Z39.88-2004&rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&rft.genre=article&rft.jtitle=Analytical+Biochemistry&rft.atitle=A+comparative+analysis+of+soft+computing+techniques+for+gene+prediction&rft.volume=438&rft.issue=1&rft.pages=14-21&rft.date=2013-07&rft_id=info%3Adoi%2F10.1016%2Fj.ab.2013.03.015&rft_id=info%3Apmid%2F23529114&rft.aulast=Goel&rft.aufirst=N&rft.au=Singh%2C+S&rft.au=Aseri%2C+TC&rfr_id=info%3Asid%2Fen.wikipedia.org%3AGene+prediction" class="Z3988"></span></span> </li> <li id="cite_note-Johansen2009-19"><span class="mw-cite-backlink"><b><a href="#cite_ref-Johansen2009_19-0">^</a></b></span> <span class="reference-text"><link rel="mw-deduplicated-inline-style" href="mw-data:TemplateStyles:r1238218222"><cite id="CITEREFJohansenRyenEftes∅lKjosmoen2009" class="citation book cs1">Johansen, ∅Ystein; Ryen, Tom; Eftes∅l, Trygve; Kjosmoen, Thomas; Ruoff, Peter (2009). "Splice Site Prediction Using Artificial Neural Networks". <i>Computational Intelligence Methods for Bioinformatics and Biostatistics</i>. Lec Not Comp Sci. Vol. 5488. pp. 102–113. <a href="/wiki/Doi_(identifier)" class="mw-redirect" title="Doi (identifier)">doi</a>:<a rel="nofollow" class="external text" href="https://doi.org/10.1007%2F978-3-642-02504-4_9">10.1007/978-3-642-02504-4_9</a>. <a href="/wiki/ISBN_(identifier)" class="mw-redirect" title="ISBN (identifier)">ISBN</a> <a href="/wiki/Special:BookSources/978-3-642-02503-7" title="Special:BookSources/978-3-642-02503-7"><bdi>978-3-642-02503-7</bdi></a>.</cite><span title="ctx_ver=Z39.88-2004&rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Abook&rft.genre=bookitem&rft.atitle=Splice+Site+Prediction+Using+Artificial+Neural+Networks&rft.btitle=Computational+Intelligence+Methods+for+Bioinformatics+and+Biostatistics&rft.series=Lec+Not+Comp+Sci&rft.pages=102-113&rft.date=2009&rft_id=info%3Adoi%2F10.1007%2F978-3-642-02504-4_9&rft.isbn=978-3-642-02503-7&rft.aulast=Johansen&rft.aufirst=%E2%88%85Ystein&rft.au=Ryen%2C+Tom&rft.au=Eftes%E2%88%85l%2C+Trygve&rft.au=Kjosmoen%2C+Thomas&rft.au=Ruoff%2C+Peter&rfr_id=info%3Asid%2Fen.wikipedia.org%3AGene+prediction" class="Z3988"></span></span> </li> <li id="cite_note-:0-20"><span class="mw-cite-backlink">^ <a href="#cite_ref-:0_20-0"><sup><i><b>a</b></i></sup></a> <a href="#cite_ref-:0_20-1"><sup><i><b>b</b></i></sup></a> <a href="#cite_ref-:0_20-2"><sup><i><b>c</b></i></sup></a></span> <span class="reference-text"><link rel="mw-deduplicated-inline-style" href="mw-data:TemplateStyles:r1238218222"><cite id="CITEREFGrossDoSirotaBatzoglou2007" class="citation journal cs1">Gross SS, Do CB, Sirota M, Batzoglou S (2007). <a rel="nofollow" class="external text" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2246271">"CONTRAST: a discriminative, phylogeny-free approach to multiple informant de novo gene prediction"</a>. <i>Genome Biology</i>. <b>8</b> (12): R269. <a href="/wiki/Doi_(identifier)" class="mw-redirect" title="Doi (identifier)">doi</a>:<span class="id-lock-free" title="Freely accessible"><a rel="nofollow" class="external text" href="https://doi.org/10.1186%2Fgb-2007-8-12-r269">10.1186/gb-2007-8-12-r269</a></span>. <a href="/wiki/PMC_(identifier)" class="mw-redirect" title="PMC (identifier)">PMC</a> <span class="id-lock-free" title="Freely accessible"><a rel="nofollow" class="external text" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2246271">2246271</a></span>. <a href="/wiki/PMID_(identifier)" class="mw-redirect" title="PMID (identifier)">PMID</a> <a rel="nofollow" class="external text" href="https://pubmed.ncbi.nlm.nih.gov/18096039">18096039</a>.</cite><span title="ctx_ver=Z39.88-2004&rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&rft.genre=article&rft.jtitle=Genome+Biology&rft.atitle=CONTRAST%3A+a+discriminative%2C+phylogeny-free+approach+to+multiple+informant+de+novo+gene+prediction&rft.volume=8&rft.issue=12&rft.pages=R269&rft.date=2007&rft_id=https%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fpmc%2Farticles%2FPMC2246271%23id-name%3DPMC&rft_id=info%3Apmid%2F18096039&rft_id=info%3Adoi%2F10.1186%2Fgb-2007-8-12-r269&rft.aulast=Gross&rft.aufirst=SS&rft.au=Do%2C+CB&rft.au=Sirota%2C+M&rft.au=Batzoglou%2C+S&rft_id=https%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fpmc%2Farticles%2FPMC2246271&rfr_id=info%3Asid%2Fen.wikipedia.org%3AGene+prediction" class="Z3988"></span></span> </li> <li id="cite_note-Alexander2010-21"><span class="mw-cite-backlink">^ <a href="#cite_ref-Alexander2010_21-0"><sup><i><b>a</b></i></sup></a> <a href="#cite_ref-Alexander2010_21-1"><sup><i><b>b</b></i></sup></a></span> <span class="reference-text"><link rel="mw-deduplicated-inline-style" href="mw-data:TemplateStyles:r1238218222"><cite id="CITEREFAlexanderFangRozowskySnyder2010" class="citation journal cs1">Alexander RP, Fang G, Rozowsky J, Snyder M, Gerstein MB (August 2010). "Annotating non-coding regions of the genome". <i>Nature Reviews. Genetics</i>. <b>11</b> (8): 559–71. <a href="/wiki/Doi_(identifier)" class="mw-redirect" title="Doi (identifier)">doi</a>:<a rel="nofollow" class="external text" href="https://doi.org/10.1038%2Fnrg2814">10.1038/nrg2814</a>. <a href="/wiki/PMID_(identifier)" class="mw-redirect" title="PMID (identifier)">PMID</a> <a rel="nofollow" class="external text" href="https://pubmed.ncbi.nlm.nih.gov/20628352">20628352</a>. <a href="/wiki/S2CID_(identifier)" class="mw-redirect" title="S2CID (identifier)">S2CID</a> <a rel="nofollow" class="external text" href="https://api.semanticscholar.org/CorpusID:6617359">6617359</a>.</cite><span title="ctx_ver=Z39.88-2004&rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&rft.genre=article&rft.jtitle=Nature+Reviews.+Genetics&rft.atitle=Annotating+non-coding+regions+of+the+genome&rft.volume=11&rft.issue=8&rft.pages=559-71&rft.date=2010-08&rft_id=https%3A%2F%2Fapi.semanticscholar.org%2FCorpusID%3A6617359%23id-name%3DS2CID&rft_id=info%3Apmid%2F20628352&rft_id=info%3Adoi%2F10.1038%2Fnrg2814&rft.aulast=Alexander&rft.aufirst=RP&rft.au=Fang%2C+G&rft.au=Rozowsky%2C+J&rft.au=Snyder%2C+M&rft.au=Gerstein%2C+MB&rfr_id=info%3Asid%2Fen.wikipedia.org%3AGene+prediction" class="Z3988"></span></span> </li> <li id="cite_note-Svensson2006-22"><span class="mw-cite-backlink"><b><a href="#cite_ref-Svensson2006_22-0">^</a></b></span> <span class="reference-text"><link rel="mw-deduplicated-inline-style" href="mw-data:TemplateStyles:r1238218222"><cite id="CITEREFSvenssonArvestadLagergren2006" class="citation journal cs1">Svensson O, Arvestad L, Lagergren J (May 2006). <a rel="nofollow" class="external text" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1456316">"Genome-wide survey for biologically functional pseudogenes"</a>. <i>PLOS Computational Biology</i>. <b>2</b> (5): e46. <a href="/wiki/Bibcode_(identifier)" class="mw-redirect" title="Bibcode (identifier)">Bibcode</a>:<a rel="nofollow" class="external text" href="https://ui.adsabs.harvard.edu/abs/2006PLSCB...2...46S">2006PLSCB...2...46S</a>. <a href="/wiki/Doi_(identifier)" class="mw-redirect" title="Doi (identifier)">doi</a>:<span class="id-lock-free" title="Freely accessible"><a rel="nofollow" class="external text" href="https://doi.org/10.1371%2Fjournal.pcbi.0020046">10.1371/journal.pcbi.0020046</a></span>. <a href="/wiki/PMC_(identifier)" class="mw-redirect" title="PMC (identifier)">PMC</a> <span class="id-lock-free" title="Freely accessible"><a rel="nofollow" class="external text" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1456316">1456316</a></span>. <a href="/wiki/PMID_(identifier)" class="mw-redirect" title="PMID (identifier)">PMID</a> <a rel="nofollow" class="external text" href="https://pubmed.ncbi.nlm.nih.gov/16680195">16680195</a>.</cite><span title="ctx_ver=Z39.88-2004&rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&rft.genre=article&rft.jtitle=PLOS+Computational+Biology&rft.atitle=Genome-wide+survey+for+biologically+functional+pseudogenes&rft.volume=2&rft.issue=5&rft.pages=e46&rft.date=2006-05&rft_id=https%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fpmc%2Farticles%2FPMC1456316%23id-name%3DPMC&rft_id=info%3Apmid%2F16680195&rft_id=info%3Adoi%2F10.1371%2Fjournal.pcbi.0020046&rft_id=info%3Abibcode%2F2006PLSCB...2...46S&rft.aulast=Svensson&rft.aufirst=O&rft.au=Arvestad%2C+L&rft.au=Lagergren%2C+J&rft_id=https%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fpmc%2Farticles%2FPMC1456316&rfr_id=info%3Asid%2Fen.wikipedia.org%3AGene+prediction" class="Z3988"></span></span> </li> <li id="cite_note-Zhang2004-23"><span class="mw-cite-backlink"><b><a href="#cite_ref-Zhang2004_23-0">^</a></b></span> <span class="reference-text"><link rel="mw-deduplicated-inline-style" href="mw-data:TemplateStyles:r1238218222"><cite id="CITEREFZhangGerstein2004" class="citation journal cs1">Zhang Z, Gerstein M (August 2004). "Large-scale analysis of pseudogenes in the human genome". <i>Current Opinion in Genetics & Development</i>. <b>14</b> (4): 328–35. <a href="/wiki/Doi_(identifier)" class="mw-redirect" title="Doi (identifier)">doi</a>:<a rel="nofollow" class="external text" href="https://doi.org/10.1016%2Fj.gde.2004.06.003">10.1016/j.gde.2004.06.003</a>. <a href="/wiki/PMID_(identifier)" class="mw-redirect" title="PMID (identifier)">PMID</a> <a rel="nofollow" class="external text" href="https://pubmed.ncbi.nlm.nih.gov/15261647">15261647</a>.</cite><span title="ctx_ver=Z39.88-2004&rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&rft.genre=article&rft.jtitle=Current+Opinion+in+Genetics+%26+Development&rft.atitle=Large-scale+analysis+of+pseudogenes+in+the+human+genome&rft.volume=14&rft.issue=4&rft.pages=328-35&rft.date=2004-08&rft_id=info%3Adoi%2F10.1016%2Fj.gde.2004.06.003&rft_id=info%3Apmid%2F15261647&rft.aulast=Zhang&rft.aufirst=Z&rft.au=Gerstein%2C+M&rfr_id=info%3Asid%2Fen.wikipedia.org%3AGene+prediction" class="Z3988"></span></span> </li> <li id="cite_note-Kelley2012-24"><span class="mw-cite-backlink"><b><a href="#cite_ref-Kelley2012_24-0">^</a></b></span> <span class="reference-text"><link rel="mw-deduplicated-inline-style" href="mw-data:TemplateStyles:r1238218222"><cite id="CITEREFKelleyLiuDelcherPop2012" class="citation journal cs1">Kelley DR, Liu B, Delcher AL, Pop M, Salzberg SL (January 2012). <a rel="nofollow" class="external text" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3245904">"Gene prediction with Glimmer for metagenomic sequences augmented by classification and clustering"</a>. <i>Nucleic Acids Research</i>. <b>40</b> (1): e9. <a href="/wiki/Doi_(identifier)" class="mw-redirect" title="Doi (identifier)">doi</a>:<a rel="nofollow" class="external text" href="https://doi.org/10.1093%2Fnar%2Fgkr1067">10.1093/nar/gkr1067</a>. <a href="/wiki/PMC_(identifier)" class="mw-redirect" title="PMC (identifier)">PMC</a> <span class="id-lock-free" title="Freely accessible"><a rel="nofollow" class="external text" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3245904">3245904</a></span>. <a href="/wiki/PMID_(identifier)" class="mw-redirect" title="PMID (identifier)">PMID</a> <a rel="nofollow" class="external text" href="https://pubmed.ncbi.nlm.nih.gov/22102569">22102569</a>.</cite><span title="ctx_ver=Z39.88-2004&rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&rft.genre=article&rft.jtitle=Nucleic+Acids+Research&rft.atitle=Gene+prediction+with+Glimmer+for+metagenomic+sequences+augmented+by+classification+and+clustering&rft.volume=40&rft.issue=1&rft.pages=e9&rft.date=2012-01&rft_id=https%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fpmc%2Farticles%2FPMC3245904%23id-name%3DPMC&rft_id=info%3Apmid%2F22102569&rft_id=info%3Adoi%2F10.1093%2Fnar%2Fgkr1067&rft.aulast=Kelley&rft.aufirst=DR&rft.au=Liu%2C+B&rft.au=Delcher%2C+AL&rft.au=Pop%2C+M&rft.au=Salzberg%2C+SL&rft_id=https%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fpmc%2Farticles%2FPMC3245904&rfr_id=info%3Asid%2Fen.wikipedia.org%3AGene+prediction" class="Z3988"></span></span> </li> <li id="cite_note-Huson2011-25"><span class="mw-cite-backlink"><b><a href="#cite_ref-Huson2011_25-0">^</a></b></span> <span class="reference-text"><link rel="mw-deduplicated-inline-style" href="mw-data:TemplateStyles:r1238218222"><cite id="CITEREFHusonMitraRuscheweyhWeber2011" class="citation journal cs1">Huson DH, Mitra S, Ruscheweyh HJ, Weber N, Schuster SC (September 2011). <a rel="nofollow" class="external text" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3166839">"Integrative analysis of environmental sequences using MEGAN4"</a>. <i>Genome Research</i>. <b>21</b> (9): 1552–60. <a href="/wiki/Doi_(identifier)" class="mw-redirect" title="Doi (identifier)">doi</a>:<a rel="nofollow" class="external text" href="https://doi.org/10.1101%2Fgr.120618.111">10.1101/gr.120618.111</a>. <a href="/wiki/PMC_(identifier)" class="mw-redirect" title="PMC (identifier)">PMC</a> <span class="id-lock-free" title="Freely accessible"><a rel="nofollow" class="external text" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3166839">3166839</a></span>. <a href="/wiki/PMID_(identifier)" class="mw-redirect" title="PMID (identifier)">PMID</a> <a rel="nofollow" class="external text" href="https://pubmed.ncbi.nlm.nih.gov/21690186">21690186</a>.</cite><span title="ctx_ver=Z39.88-2004&rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&rft.genre=article&rft.jtitle=Genome+Research&rft.atitle=Integrative+analysis+of+environmental+sequences+using+MEGAN4&rft.volume=21&rft.issue=9&rft.pages=1552-60&rft.date=2011-09&rft_id=https%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fpmc%2Farticles%2FPMC3166839%23id-name%3DPMC&rft_id=info%3Apmid%2F21690186&rft_id=info%3Adoi%2F10.1101%2Fgr.120618.111&rft.aulast=Huson&rft.aufirst=DH&rft.au=Mitra%2C+S&rft.au=Ruscheweyh%2C+HJ&rft.au=Weber%2C+N&rft.au=Schuster%2C+SC&rft_id=https%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fpmc%2Farticles%2FPMC3166839&rfr_id=info%3Asid%2Fen.wikipedia.org%3AGene+prediction" class="Z3988"></span></span> </li> <li id="cite_note-Zhu2010-26"><span class="mw-cite-backlink"><b><a href="#cite_ref-Zhu2010_26-0">^</a></b></span> <span class="reference-text"><link rel="mw-deduplicated-inline-style" href="mw-data:TemplateStyles:r1238218222"><cite id="CITEREFZhuLomsadzeBorodovsky2010" class="citation journal cs1">Zhu W, Lomsadze A, Borodovsky M (July 2010). <a rel="nofollow" class="external text" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2896542">"Ab initio gene identification in metagenomic sequences"</a>. <i>Nucleic Acids Research</i>. <b>38</b> (12): e132. <a href="/wiki/Doi_(identifier)" class="mw-redirect" title="Doi (identifier)">doi</a>:<a rel="nofollow" class="external text" href="https://doi.org/10.1093%2Fnar%2Fgkq275">10.1093/nar/gkq275</a>. <a href="/wiki/PMC_(identifier)" class="mw-redirect" title="PMC (identifier)">PMC</a> <span class="id-lock-free" title="Freely accessible"><a rel="nofollow" class="external text" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2896542">2896542</a></span>. <a href="/wiki/PMID_(identifier)" class="mw-redirect" title="PMID (identifier)">PMID</a> <a rel="nofollow" class="external text" href="https://pubmed.ncbi.nlm.nih.gov/20403810">20403810</a>.</cite><span title="ctx_ver=Z39.88-2004&rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&rft.genre=article&rft.jtitle=Nucleic+Acids+Research&rft.atitle=Ab+initio+gene+identification+in+metagenomic+sequences&rft.volume=38&rft.issue=12&rft.pages=e132&rft.date=2010-07&rft_id=https%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fpmc%2Farticles%2FPMC2896542%23id-name%3DPMC&rft_id=info%3Apmid%2F20403810&rft_id=info%3Adoi%2F10.1093%2Fnar%2Fgkq275&rft.aulast=Zhu&rft.aufirst=W&rft.au=Lomsadze%2C+A&rft.au=Borodovsky%2C+M&rft_id=https%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fpmc%2Farticles%2FPMC2896542&rfr_id=info%3Asid%2Fen.wikipedia.org%3AGene+prediction" class="Z3988"></span></span> </li> </ol></div></div> <div class="mw-heading mw-heading2"><h2 id="External_links">External links</h2><span class="mw-editsection"><span class="mw-editsection-bracket">[</span><a href="/w/index.php?title=Gene_prediction&action=edit&section=12" title="Edit section: External links"><span>edit</span></a><span class="mw-editsection-bracket">]</span></span></div> <ul><li><a rel="nofollow" class="external text" href="http://bioinf.uni-greifswald.de/webaugustus/">Augustus</a></li> <li><a rel="nofollow" class="external text" href="http://linux1.softberry.com/berry.phtml?topic=fgenesh&group=programs&subgroup=gfind">FGENESH</a> <a rel="nofollow" class="external text" href="https://archive.today/20130104183453/http://linux1.softberry.com/berry.phtml?topic=fgenesh&group=programs&subgroup=gfind">Archived</a> 2013-01-04 at <a href="/wiki/Archive.today" title="Archive.today">archive.today</a></li> <li><a rel="nofollow" class="external text" href="http://www.jstacs.de/index.php/GeMoMa">GeMoMa</a> - Homology-based gene prediction based on amino acid and intron position conservation as well as RNA-Seq data</li> <li><a rel="nofollow" class="external text" href="http://genome.imim.es/software/geneid/">geneid</a>, <a rel="nofollow" class="external text" href="http://genome.imim.es/software/sgp2/">SGP2</a></li> <li><a rel="nofollow" class="external text" href="http://cbcb.umd.edu/software/glimmer">Glimmer</a> <a rel="nofollow" class="external text" href="https://web.archive.org/web/20110826005802/http://www.cbcb.umd.edu/software/glimmer/">Archived</a> 2011-08-26 at the <a href="/wiki/Wayback_Machine" title="Wayback Machine">Wayback Machine</a>, <a rel="nofollow" class="external text" href="http://cbcb.umd.edu/software/GlimmerHMM">GlimmerHMM</a> <a rel="nofollow" class="external text" href="https://web.archive.org/web/20110818235355/http://www.cbcb.umd.edu/software/GlimmerHMM/">Archived</a> 2011-08-18 at the <a href="/wiki/Wayback_Machine" title="Wayback Machine">Wayback Machine</a></li> <li><a rel="nofollow" class="external text" href="https://web.archive.org/web/20061116041807/http://www.genomethreader.org/">GenomeThreader</a></li> <li><a rel="nofollow" class="external text" href="http://www.scfbio-iitd.res.in/research/genepredictor.htm">ChemGenome</a></li> <li><a rel="nofollow" class="external text" href="http://opal.biology.gatech.edu/GeneMark/">GeneMark</a></li> <li><a rel="nofollow" class="external text" href="https://web.archive.org/web/20080915090738/http://www.cebitec.uni-bielefeld.de/groups/brf/software/gismo/">Gismo</a></li> <li><a rel="nofollow" class="external text" href="http://www.mgene.org/">mGene</a></li> <li><a rel="nofollow" class="external text" href="http://web.mit.edu/star/orf/">StarORF</a> — A multi-platform and web tool for predicting ORFs and obtaining reverse complement sequence</li> <li><a rel="nofollow" class="external text" href="http://www.yandell-lab.org/software/maker.html">Maker</a> - A portable and easily configurable genome annotation pipeline</li></ul> <div class="navbox-styles"><style data-mw-deduplicate="TemplateStyles:r1129693374">.mw-parser-output .hlist dl,.mw-parser-output .hlist ol,.mw-parser-output .hlist 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.navbar{display:none!important}}</style><div class="navbar plainlinks hlist navbar-mini"><ul><li class="nv-view"><a href="/wiki/Template:Genomics" title="Template:Genomics"><abbr title="View this template">v</abbr></a></li><li class="nv-talk"><a href="/wiki/Template_talk:Genomics" title="Template talk:Genomics"><abbr title="Discuss this template">t</abbr></a></li><li class="nv-edit"><a href="/wiki/Special:EditPage/Template:Genomics" title="Special:EditPage/Template:Genomics"><abbr title="Edit this template">e</abbr></a></li></ul></div><div id="Genomics" style="font-size:114%;margin:0 4em"><a href="/wiki/Genomics" title="Genomics">Genomics</a></div></th></tr><tr><th scope="row" class="navbox-group" style="width:1%">Fields</th><td class="navbox-list-with-group navbox-list navbox-odd" style="width:100%;padding:0"><div style="padding:0 0.25em"> <ul><li><a href="/wiki/Cognitive_genomics" title="Cognitive genomics">Cognitive genomics</a></li> <li><a href="/wiki/Computational_genomics" title="Computational genomics">Computational genomics</a></li> <li><a href="/wiki/Comparative_genomics" title="Comparative genomics">Comparative genomics</a></li> <li><a href="/wiki/Functional_genomics" title="Functional genomics">Functional genomics</a></li> <li><a href="/wiki/Genome_project" title="Genome project">Genome project</a> <ul><li><a href="/wiki/Human_Genome_Project" title="Human Genome Project">Human Genome Project</a></li></ul></li> <li><a href="/wiki/Metagenomics" title="Metagenomics">Metagenomics</a> <ul><li><a href="/wiki/Human_Microbiome_Project" title="Human Microbiome Project">Human Microbiome Project</a></li></ul></li> <li><a href="/wiki/Pangenomics" class="mw-redirect" title="Pangenomics">Pangenomics</a></li> <li><a href="/wiki/Personal_genomics" title="Personal genomics">Personal genomics</a></li> <li><a href="/wiki/Population_genomics" title="Population genomics">Population genomics</a></li> <li><a href="/wiki/Sociogenomics" title="Sociogenomics"><i>Socio</i>genomics</a></li> <li><a href="/wiki/Structural_genomics" title="Structural genomics">Structural genomics</a></li></ul> </div></td></tr><tr><th scope="row" class="navbox-group" style="width:1%"><a href="/wiki/Bioinformatics" title="Bioinformatics">Bioinformatics</a></th><td class="navbox-list-with-group navbox-list navbox-even" style="width:100%;padding:0"><div style="padding:0 0.25em"> <ul><li><a href="/wiki/Biochip" title="Biochip">Biochip</a></li> <li><a href="/wiki/Cheminformatics" title="Cheminformatics">Cheminformatics</a></li> <li><a href="/wiki/Chemogenomics" title="Chemogenomics">Chemogenomics</a></li> <li><a href="/wiki/Connectomics" title="Connectomics">Connectomics</a> <ul><li><a href="/wiki/Human_Connectome_Project" title="Human Connectome Project">Human Connectome Project</a></li></ul></li> <li><a href="/wiki/Epigenomics" title="Epigenomics">Epigenomics</a> <ul><li><a href="/wiki/Human_Epigenome_Project" title="Human Epigenome Project">Human Epigenome Project</a></li></ul></li> <li><a href="/wiki/Glycomics" title="Glycomics">Glycomics</a></li> <li><a href="/wiki/Immunomics" title="Immunomics">Immunomics</a></li> <li><a href="/wiki/Lipidomics" title="Lipidomics">Lipidomics</a></li> <li><a href="/wiki/Metabolomics" title="Metabolomics">Metabolomics</a></li> <li><a href="/wiki/Microbiome" title="Microbiome">Microbiomics</a></li> <li><a href="/wiki/Nutrigenomics" class="mw-redirect" title="Nutrigenomics">Nutrigenomics</a></li> <li><a href="/wiki/Paleopolyploidy" title="Paleopolyploidy">Paleopolyploidy</a></li> <li><a href="/wiki/Pharmacogenetics" class="mw-redirect" title="Pharmacogenetics">Pharmacogenetics</a></li> <li><a href="/wiki/Pharmacogenomics" title="Pharmacogenomics">Pharmacogenomics</a></li> <li><a href="/wiki/Systems_biology" title="Systems biology">Systems biology</a></li> <li><a href="/wiki/Toxicogenomics" title="Toxicogenomics">Toxicogenomics</a></li> <li><a href="/wiki/Transcriptomics" class="mw-redirect" title="Transcriptomics">Transcriptomics</a></li></ul> </div></td></tr><tr><th scope="row" class="navbox-group" style="width:1%"><a href="/wiki/Structural_biology" title="Structural biology">Structural biology</a></th><td class="navbox-list-with-group navbox-list navbox-odd" style="width:100%;padding:0"><div style="padding:0 0.25em"> <ul><li><a href="/wiki/Proteomics" title="Proteomics">Proteomics</a> <ul><li><a href="/wiki/Human_proteome_project" class="mw-redirect" title="Human proteome project">Human proteome project</a></li></ul></li> <li><a href="/wiki/Call-map_proteomics" class="mw-redirect" title="Call-map proteomics">Call-map proteomics</a></li> <li><a href="/wiki/Structure-based_drug_design" class="mw-redirect" title="Structure-based drug design">Structure-based drug design</a></li> <li><a href="/wiki/Expression_proteomics" class="mw-redirect" title="Expression proteomics">Expression proteomics</a></li></ul> </div></td></tr><tr><th scope="row" class="navbox-group" style="width:1%">Research tools</th><td class="navbox-list-with-group navbox-list navbox-even" style="width:100%;padding:0"><div style="padding:0 0.25em"> <ul><li><a href="/wiki/2-D_electrophoresis" class="mw-redirect" title="2-D electrophoresis">2-D electrophoresis</a></li> <li><a href="/wiki/Mass_spectrometer" class="mw-redirect" title="Mass spectrometer">Mass spectrometer</a></li> <li><a href="/wiki/Electrospray_ionization" title="Electrospray ionization">Electrospray ionization</a></li> <li><a href="/wiki/Matrix-assisted_laser_desorption_ionization" class="mw-redirect" title="Matrix-assisted laser desorption ionization">Matrix-assisted laser desorption ionization</a></li> <li><a href="/wiki/Matrix-assisted_laser_desorption_ionization-time_of_flight_mass_spectrometer" class="mw-redirect" title="Matrix-assisted laser desorption ionization-time of flight mass spectrometer">Matrix-assisted laser desorption ionization-time of flight mass spectrometer</a></li> <li><a href="/wiki/Microfluidic-based_tools" class="mw-redirect" title="Microfluidic-based tools">Microfluidic-based tools</a></li> <li><a href="/wiki/Isotope_affinity_tags" class="mw-redirect" title="Isotope affinity tags">Isotope affinity tags</a></li> <li><a href="/wiki/Chromosome_conformation_capture" title="Chromosome conformation capture">Chromosome conformation capture</a></li></ul> </div></td></tr><tr><th scope="row" class="navbox-group" style="width:1%">Organizations</th><td class="navbox-list-with-group navbox-list navbox-odd" style="width:100%;padding:0"><div style="padding:0 0.25em"> <ul><li><a href="/wiki/DNA_Data_Bank_of_Japan" title="DNA Data Bank of Japan">DNA Data Bank of Japan</a> (JP)</li> <li><a href="/wiki/European_Molecular_Biology_Laboratory" title="European Molecular Biology Laboratory">European Molecular Biology Laboratory</a> (EU)</li> <li><a href="/wiki/National_Institutes_of_Health" title="National Institutes of Health">National Institutes of Health</a> (USA)</li> <li><a href="/wiki/Wellcome_Sanger_Institute" title="Wellcome Sanger Institute">Wellcome Sanger Institute</a> (UK)</li></ul> </div></td></tr><tr><td class="navbox-abovebelow" colspan="2"><div> <ul><li><span class="noviewer" typeof="mw:File"><span title="List-Class article"><img alt="" src="//upload.wikimedia.org/wikipedia/en/thumb/d/db/Symbol_list_class.svg/16px-Symbol_list_class.svg.png" decoding="async" width="16" height="16" class="mw-file-element" srcset="//upload.wikimedia.org/wikipedia/en/thumb/d/db/Symbol_list_class.svg/23px-Symbol_list_class.svg.png 1.5x, //upload.wikimedia.org/wikipedia/en/thumb/d/db/Symbol_list_class.svg/31px-Symbol_list_class.svg.png 2x" data-file-width="180" data-file-height="185" /></span></span> <b><a href="/wiki/List_of_omics_topics_in_biology" title="List of omics topics in biology">List</a> </b></li> <li><span class="noviewer" typeof="mw:File"><span title="Category"><img alt="" src="//upload.wikimedia.org/wikipedia/en/thumb/9/96/Symbol_category_class.svg/16px-Symbol_category_class.svg.png" decoding="async" width="16" height="16" class="mw-file-element" srcset="//upload.wikimedia.org/wikipedia/en/thumb/9/96/Symbol_category_class.svg/23px-Symbol_category_class.svg.png 1.5x, //upload.wikimedia.org/wikipedia/en/thumb/9/96/Symbol_category_class.svg/31px-Symbol_category_class.svg.png 2x" data-file-width="180" data-file-height="185" /></span></span> <b><a href="/wiki/Category:Omics" title="Category:Omics">Category</a></b></li></ul> </div></td></tr></tbody></table></div> <div class="navbox-styles"><link rel="mw-deduplicated-inline-style" href="mw-data:TemplateStyles:r1129693374"><link rel="mw-deduplicated-inline-style" href="mw-data:TemplateStyles:r1236075235"></div><div role="navigation" class="navbox" aria-labelledby="Branches_of_biology" style="padding:3px"><table class="nowraplinks mw-collapsible autocollapse navbox-inner" style="border-spacing:0;background:transparent;color:inherit"><tbody><tr><th scope="col" class="navbox-title" colspan="2"><link rel="mw-deduplicated-inline-style" href="mw-data:TemplateStyles:r1129693374"><link rel="mw-deduplicated-inline-style" href="mw-data:TemplateStyles:r1239400231"><div class="navbar plainlinks hlist navbar-mini"><ul><li class="nv-view"><a href="/wiki/Template:Branches_of_biology" title="Template:Branches of biology"><abbr title="View this template">v</abbr></a></li><li class="nv-talk"><a href="/wiki/Template_talk:Branches_of_biology" title="Template talk:Branches of biology"><abbr title="Discuss this template">t</abbr></a></li><li class="nv-edit"><a href="/wiki/Special:EditPage/Template:Branches_of_biology" title="Special:EditPage/Template:Branches of biology"><abbr title="Edit this template">e</abbr></a></li></ul></div><div id="Branches_of_biology" style="font-size:114%;margin:0 4em"><a href="/wiki/Outline_of_biology#Branches" title="Outline of biology">Branches of biology</a></div></th></tr><tr><td colspan="2" class="navbox-list navbox-odd hlist" style="width:100%;padding:0"><div style="padding:0 0.25em"> <ul><li><a href="/wiki/Abiogenesis" title="Abiogenesis">Abiogenesis</a></li> <li><a href="/wiki/Aerobiology" title="Aerobiology">Aerobiology</a></li> <li><a href="/wiki/Agronomy" title="Agronomy">Agronomy</a></li> <li><a href="/wiki/Agrostology" title="Agrostology">Agrostology</a></li> <li><a href="/wiki/Anatomy" title="Anatomy">Anatomy</a></li> <li><a href="/wiki/Astrobiology" title="Astrobiology">Astrobiology</a></li> <li><a href="/wiki/Bacteriology" title="Bacteriology">Bacteriology</a></li> <li><a href="/wiki/Biochemistry" title="Biochemistry">Biochemistry</a></li> <li><a href="/wiki/Biogeography" title="Biogeography">Biogeography</a></li> <li><a href="/wiki/Biogeology" title="Biogeology">Biogeology</a></li> <li><a href="/wiki/Bioinformatics" title="Bioinformatics">Bioinformatics</a></li> <li><a href="/wiki/Biological_engineering" title="Biological engineering">Biological engineering</a></li> <li><a href="/wiki/Biomechanics" title="Biomechanics">Biomechanics</a></li> <li><a href="/wiki/Biophysics" title="Biophysics">Biophysics</a></li> <li><a href="/wiki/Biosemiotics" title="Biosemiotics">Biosemiotics</a></li> <li><a href="/wiki/Biostatistics" title="Biostatistics">Biostatistics</a></li> <li><a href="/wiki/Biotechnology" title="Biotechnology">Biotechnology</a></li> <li><a href="/wiki/Botany" title="Botany">Botany</a></li> <li><a href="/wiki/Cell_biology" title="Cell biology">Cell biology</a></li> <li><a href="/wiki/Cellular_microbiology" title="Cellular microbiology">Cellular microbiology</a></li> <li><a href="/wiki/Chemical_biology" title="Chemical biology">Chemical biology</a></li> <li><a href="/wiki/Chronobiology" title="Chronobiology">Chronobiology</a></li> <li><a href="/wiki/Cognitive_biology" title="Cognitive biology">Cognitive biology</a></li> <li><a href="/wiki/Computational_biology" title="Computational biology">Computational biology</a></li> <li><a href="/wiki/Conservation_biology" title="Conservation biology">Conservation biology</a></li> <li><a href="/wiki/Cryobiology" title="Cryobiology">Cryobiology</a></li> <li><a href="/wiki/Cytogenetics" title="Cytogenetics">Cytogenetics</a></li> <li><a href="/wiki/Dendrology" title="Dendrology">Dendrology</a></li> <li><a href="/wiki/Developmental_biology" title="Developmental biology">Developmental biology</a></li> <li><a href="/wiki/Ecological_genetics" title="Ecological genetics">Ecological genetics</a></li> <li><a href="/wiki/Ecology" title="Ecology">Ecology</a></li> <li><a href="/wiki/Embryology" title="Embryology">Embryology</a></li> <li><a href="/wiki/Epidemiology" title="Epidemiology">Epidemiology</a></li> <li><a href="/wiki/Epigenetics" title="Epigenetics">Epigenetics</a></li> <li><a href="/wiki/Evolutionary_biology" title="Evolutionary biology">Evolutionary biology</a></li> <li><a href="/wiki/Freshwater_biology" title="Freshwater 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