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<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd"> <html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en" dir="ltr"> <head><script type="text/javascript" src="/_static/js/bundle-playback.js?v=HxkREWBo" charset="utf-8"></script> <script type="text/javascript" src="/_static/js/wombat.js?v=txqj7nKC" charset="utf-8"></script> <script>window.RufflePlayer=window.RufflePlayer||{};window.RufflePlayer.config={"autoplay":"on","unmuteOverlay":"hidden"};</script> <script type="text/javascript" src="/_static/js/ruffle/ruffle.js"></script> <script type="text/javascript"> __wm.init("https://web.archive.org/web"); __wm.wombat("http://wikiomics.org/wiki/List_of_articles","20070707152120","https://web.archive.org/","web","/_static/", "1183821680"); </script> <link rel="stylesheet" type="text/css" href="/_static/css/banner-styles.css?v=S1zqJCYt" /> <link rel="stylesheet" type="text/css" href="/_static/css/iconochive.css?v=3PDvdIFv" />  <meta http-equiv="Content-Type" content="text/html; charset=utf-8"/> <meta name="KEYWORDS" content="List of articles"/> <meta name="robots" content="index,follow"/> <link rel="shortcut icon" href="/web/20070707152120im_/http://wikiomics.org/favicon.ico"/> <link title="Creative Commons" type="application/rdf+xml" href="/index.php?title=List_of_articles&action=creativecommons" rel="meta"/> <link rel="copyright" href="https://web.archive.org/web/20070707152120/http://www.gnu.org/copyleft/fdl.html"/> <title>List of articles - Wikiomics Bioinformatics Wiki</title> <style type="text/css" media="screen,projection">/*<![CDATA[*/ @import "/web/20070707152120cs_/http://wikiomics.org/skins/monobook/main.css"; /*]]>*/</style> <link rel="stylesheet" type="text/css" media="print" href="/web/20070707152120cs_/http://wikiomics.org/skins/common/commonPrint.css"/>     <script type="text/javascript" src="/web/20070707152120js_/http://wikiomics.org/index.php?title=-&action=raw&gen=js"></script> <script type="text/javascript" src="/web/20070707152120js_/http://wikiomics.org/skins/common/wikibits.js"></script> <style type="text/css">/*<![CDATA[*/ @import "/web/20070707152120cs_/http://wikiomics.org/index.php?title=MediaWiki:Monobook.css&action=raw&ctype=text/css&smaxage=18000"; @import "/web/20070707152120cs_/http://wikiomics.org/index.php?title=-&action=raw&gen=css&maxage=18000"; /*]]>*/</style> </head> <body class="ns-0"> <div id="globalWrapper"> <div id="column-content"> <div id="content"> <a name="top" id="top"></a> <h1 class="firstHeading">List of articles</h1> <div id="bodyContent"> <h3 id="siteSub">From Wikiomics</h3> <div id="contentSub"></div>  <p>This is the list of the most important articles of this wiki. If you create an article in this wiki, just insert a link on this page. Not all articles need to be listed here, just do what feels right. There is also a space for wanted articles. Also, see <a href="/web/20070707152120/http://wikiomics.org/wiki/Special:Categories" title="Special:Categories">Special:Categories</a> for all the categories which are used to tag articles, and <a href="/web/20070707152120/http://wikiomics.org/wiki/Special:Allpages" title="Special:Allpages">Special:Allpages</a> for all the pages. </p> <table id="toc" class="toc"><tr><td><div id="toctitle"><h2>Contents</h2></div> <ul> <li class="toclevel-1"><a href="#General"><span class="tocnumber">1</span> <span class="toctext">General</span></a></li> <li class="toclevel-1"><a href="#Sequence_analysis"><span class="tocnumber">2</span> <span class="toctext">Sequence analysis</span></a></li> <li class="toclevel-1"><a href="#Proteins"><span class="tocnumber">3</span> <span class="toctext">Proteins</span></a> <ul> <li class="toclevel-2"><a href="#Protein_structure"><span class="tocnumber">3.1</span> <span class="toctext">Protein structure</span></a></li> </ul> </li> <li class="toclevel-1"><a href="#RNA"><span class="tocnumber">4</span> <span class="toctext">RNA</span></a></li> <li class="toclevel-1"><a href="#Phylogenetics"><span class="tocnumber">5</span> <span class="toctext">Phylogenetics</span></a></li> <li class="toclevel-1"><a href="#Microarrays"><span class="tocnumber">6</span> <span class="toctext">Microarrays</span></a></li> <li class="toclevel-1"><a href="#SNP_and_CGH_Data"><span class="tocnumber">7</span> <span class="toctext">SNP and CGH Data</span></a></li> <li class="toclevel-1"><a href="#Chromatin_Immunoprecipitation"><span class="tocnumber">8</span> <span class="toctext">Chromatin Immunoprecipitation</span></a></li> <li class="toclevel-1"><a href="#Proteomics"><span class="tocnumber">9</span> <span class="toctext">Proteomics</span></a></li> <li class="toclevel-1"><a href="#Genome_Annotation"><span class="tocnumber">10</span> <span class="toctext">Genome Annotation</span></a></li> <li class="toclevel-1"><a href="#Viruses"><span class="tocnumber">11</span> <span class="toctext">Viruses</span></a></li> <li class="toclevel-1"><a href="#Linux"><span class="tocnumber">12</span> <span class="toctext">Linux</span></a></li> <li class="toclevel-1"><a href="#Bioinformatics_and_databases"><span class="tocnumber">13</span> <span class="toctext">Bioinformatics and databases</span></a></li> <li class="toclevel-1"><a href="#Large-scale_and_intensive_computing"><span class="tocnumber">14</span> <span class="toctext">Large-scale and intensive computing</span></a></li> <li class="toclevel-1"><a href="#Communities_and_labs"><span class="tocnumber">15</span> <span class="toctext">Communities and labs</span></a></li> <li class="toclevel-1"><a href="#External_Medical_Reference_Links"><span class="tocnumber">16</span> <span class="toctext">External Medical Reference Links</span></a></li> <li class="toclevel-1"><a href="#Wikiforum:_open_questions_and_wanted_articles"><span class="tocnumber">17</span> <span class="toctext">Wikiforum: open questions and wanted articles</span></a></li> </ul> </td></tr></table> <p><script type="text/javascript"> if (window.showTocToggle) { var tocShowText = "show"; var tocHideText = "hide"; showTocToggle(); } </script> </p> <div class="editsection" style="float:right;margin-left:5px;">[<a href="/web/20070707152120/http://wikiomics.org/index.php?title=List_of_articles&action=edit&section=1" title="List of articles">edit</a>]</div><a name="General"></a><h2> General </h2> <ul><li> What is <a href="/web/20070707152120/http://wikiomics.org/wiki/Bioinformatics" title="Bioinformatics">bioinformatics</a>? </li><li> <a href="/web/20070707152120/http://wikiomics.org/wiki/Bioinfo_tutorial" title="Bioinfo tutorial">Bioinformatics tutorial</a> </li><li> External <a href="/web/20070707152120/http://wikiomics.org/wiki/Collections_of_bioinformatics_links" title="Collections of bioinformatics links">collections of bioinformatics links</a> which are well-maintained and recognized as useful by biologists </li><li> <a href="/web/20070707152120/http://wikiomics.org/wiki/Other_wikis_and_forums" title="Other wikis and forums">Other wikis and forums</a> in the field of bioinformatics </li><li> <a href="/web/20070707152120/http://wikiomics.org/wiki/Bioinformatics_journals" title="Bioinformatics journals">Bioinformatics journals</a>: what they provide and where to submit (new) </li><li> <a href="/web/20070707152120/http://wikiomics.org/wiki/Cool_links" title="Cool links">Cool links</a>: links to bioinformatics-related projects, documents or communities of special interest. </li></ul> <div class="editsection" style="float:right;margin-left:5px;">[<a href="/web/20070707152120/http://wikiomics.org/index.php?title=List_of_articles&action=edit&section=2" title="List of articles">edit</a>]</div><a name="Sequence_analysis"></a><h2> Sequence analysis </h2> <ul><li> <a href="/web/20070707152120/http://wikiomics.org/wiki/BLAST" title="BLAST"> Practical guide to BLAST</a> and its different flavors </li><li> <a href="/web/20070707152120/http://wikiomics.org/wiki/Percentage_identity" title="Percentage identity"> How to compute the percentage identity between a pair of sequences?</a> </li><li> <a href="/web/20070707152120/http://wikiomics.org/wiki/Multiple_sequence_alignment" title="Multiple sequence alignment"> How to deal with the multiple sequence alignment?</a> </li></ul> <div class="editsection" style="float:right;margin-left:5px;">[<a href="/web/20070707152120/http://wikiomics.org/index.php?title=List_of_articles&action=edit&section=3" title="List of articles">edit</a>]</div><a name="Proteins"></a><h2> Proteins </h2> <ul><li> Techniques and resources for automated <a href="/web/20070707152120/http://wikiomics.org/wiki/Protein_function_prediction" title="Protein function prediction">protein function prediction</a> </li><li> <a href="/web/20070707152120/http://wikiomics.org/wiki/BLAST" title="BLAST"> Practical guide to BLAST</a> and its different flavors </li><li> In-silico simulation of <a href="/web/20070707152120/http://wikiomics.org/wiki/Site_Directed_Mutagenesis" title="Site Directed Mutagenesis">Site Directed Mutagenesis</a> procedure or how to find best targets </li></ul> <div class="editsection" style="float:right;margin-left:5px;">[<a href="/web/20070707152120/http://wikiomics.org/index.php?title=List_of_articles&action=edit&section=4" title="List of articles">edit</a>]</div><a name="Protein_structure"></a><h3> Protein structure </h3> <ul><li> <a href="/web/20070707152120/http://wikiomics.org/wiki/Searching_for_3D_functional_sites_in_a_protein_structure" title="Searching for 3D functional sites in a protein structure">Searching for 3D functional sites in a protein structure</a> without any requirement of sequence or fold similarity </li><li> <a href="/web/20070707152120/http://wikiomics.org/wiki/RMSD" title="RMSD">RMSD</a> howto </li><li> <a href="/web/20070707152120/http://wikiomics.org/wiki/PDB_File_Howto" title="PDB File Howto">PDB File Howto</a> </li><li> <a href="/web/20070707152120/http://wikiomics.org/wiki/Protein_volume" title="Protein volume">Protein volume</a>: definitions and tools </li></ul> <div class="editsection" style="float:right;margin-left:5px;">[<a href="/web/20070707152120/http://wikiomics.org/index.php?title=List_of_articles&action=edit&section=5" title="List of articles">edit</a>]</div><a name="RNA"></a><h2> RNA </h2> <ul><li> <a href="/web/20070707152120/http://wikiomics.org/wiki/RNA_secondary_structure_prediction" title="RNA secondary structure prediction">RNA secondary structure prediction</a> <ul><li> Single sequence folding </li><li> Structures from alignments </li><li> Simultaneous alignment and structure prediction </li><li> Aligning RNA structures </li></ul> </li><li> <a href="/web/20070707152120/http://wikiomics.org/wiki/RNA_homology_search" title="RNA homology search">RNA homology search</a> <ul><li> Probabilistic methods (SCFG/CM and HMMs) </li><li> Descriptor-based methods </li><li> Family specific methods (eg. tRNAs, miRNAs) </li></ul> </li><li> <a href="/web/20070707152120/http://wikiomics.org/wiki/RNA_gene-finding" title="RNA gene-finding">RNA gene-finding</a> </li><li> <a href="/web/20070707152120/http://wikiomics.org/wiki/RNA_databases" title="RNA databases">RNA databases</a> <ul><li> Sequence databases </li><li> Alignment and consensus secondary structure databases </li><li> Tertiary structure databases </li></ul> </li><li> <a href="/web/20070707152120/http://wikiomics.org/wiki/RNA_phylogenetics" title="RNA phylogenetics">RNA phylogenetics</a> </li><li> <a href="/web/20070707152120/http://wikiomics.org/wiki/Alignment_visualization_and_plotting_RNA_structures" title="Alignment visualization and plotting RNA structures">Alignment visualization and plotting RNA structures</a> </li><li> <a href="/web/20070707152120/http://wikiomics.org/wiki/RNA_Tertiary_structure_prediction" title="RNA Tertiary structure prediction">RNA Tertiary structure prediction</a> </li></ul> <div class="editsection" style="float:right;margin-left:5px;">[<a href="/web/20070707152120/http://wikiomics.org/index.php?title=List_of_articles&action=edit&section=6" title="List of articles">edit</a>]</div><a name="Phylogenetics"></a><h2> Phylogenetics </h2> <ul><li> <a href="/web/20070707152120/http://wikiomics.org/wiki/Building_phylogenetic_trees" title="Building phylogenetic trees">Building phylogenetic trees</a> </li><li> <a href="/web/20070707152120/http://wikiomics.org/wiki/Phylogenetic_databases" title="Phylogenetic databases">Phylogenetic databases</a> </li></ul> <div class="editsection" style="float:right;margin-left:5px;">[<a href="/web/20070707152120/http://wikiomics.org/index.php?title=List_of_articles&action=edit&section=7" title="List of articles">edit</a>]</div><a name="Microarrays"></a><h2> Microarrays </h2> <ul><li> <a href="/web/20070707152120/http://wikiomics.org/wiki/Exon_microarrays" title="Exon microarrays">Exon_microarrays</a> </li><li> <a href="/web/20070707152120/http://wikiomics.org/index.php?title=Quality_Control&action=edit" class="new" title="Quality Control">Quality Control</a> </li><li> <a href="/web/20070707152120/http://wikiomics.org/index.php?title=Background_subtraction&action=edit" class="new" title="Background subtraction">Background subtraction</a> </li><li> <a href="/web/20070707152120/http://wikiomics.org/index.php?title=Microarray_normalization&action=edit" class="new" title="Microarray normalization">Microarray normalization</a> </li><li> <a href="/web/20070707152120/http://wikiomics.org/index.php?title=Statistical_Modeling&action=edit" class="new" title="Statistical Modeling">Statistical Modeling</a> </li><li> <a href="/web/20070707152120/http://wikiomics.org/index.php?title=Dimension_reduction&action=edit" class="new" title="Dimension reduction">Dimension reduction</a> </li><li> <a href="/web/20070707152120/http://wikiomics.org/index.php?title=Annotation&action=edit" class="new" title="Annotation">Annotation</a> </li><li> <a href="/web/20070707152120/http://wikiomics.org/index.php?title=Inferences&action=edit" class="new" title="Inferences">Inferences</a> </li></ul> <div class="editsection" style="float:right;margin-left:5px;">[<a href="/web/20070707152120/http://wikiomics.org/index.php?title=List_of_articles&action=edit&section=8" title="List of articles">edit</a>]</div><a name="SNP_and_CGH_Data"></a><h2> SNP and CGH Data </h2> <ul><li> <a href="/web/20070707152120/http://wikiomics.org/index.php?title=Quality_Control&action=edit" class="new" title="Quality Control">Quality Control</a> </li><li> <a href="/web/20070707152120/http://wikiomics.org/index.php?title=Background_subtraction&action=edit" class="new" title="Background subtraction">Background subtraction</a> </li><li> <a href="/web/20070707152120/http://wikiomics.org/index.php?title=Normalization&action=edit" class="new" title="Normalization">Normalization</a> </li><li> <a href="/web/20070707152120/http://wikiomics.org/index.php?title=Integration_with_Microarray_data_analysis&action=edit" class="new" title="Integration with Microarray data analysis">Integration with Microarray data analysis</a> </li></ul> <div class="editsection" style="float:right;margin-left:5px;">[<a href="/web/20070707152120/http://wikiomics.org/index.php?title=List_of_articles&action=edit&section=9" title="List of articles">edit</a>]</div><a name="Chromatin_Immunoprecipitation"></a><h2> Chromatin Immunoprecipitation </h2> <ul><li> <a href="/web/20070707152120/http://wikiomics.org/wiki/ChIP-chip" title="ChIP-chip">ChIP-chip Analysis Software</a> </li></ul> <div class="editsection" style="float:right;margin-left:5px;">[<a href="/web/20070707152120/http://wikiomics.org/index.php?title=List_of_articles&action=edit&section=10" title="List of articles">edit</a>]</div><a name="Proteomics"></a><h2> Proteomics </h2> <ul><li> <a href="/web/20070707152120/http://wikiomics.org/wiki/Protein_mass_spectrometry" title="Protein mass spectrometry">Protein mass spectrometry</a> </li><li> <a href="/web/20070707152120/http://wikiomics.org/index.php?title=Protein_microarray&action=edit" class="new" title="Protein microarray">Protein microarray</a> </li></ul> <div class="editsection" style="float:right;margin-left:5px;">[<a href="/web/20070707152120/http://wikiomics.org/index.php?title=List_of_articles&action=edit&section=11" title="List of articles">edit</a>]</div><a name="Genome_Annotation"></a><h2> Genome Annotation </h2> <ul><li> <a href="/web/20070707152120/http://wikiomics.org/wiki/Viewing_and_sharing_genome_annotations" title="Viewing and sharing genome annotations">Viewing and sharing genome annotations</a> </li><li> <a href="/web/20070707152120/http://wikiomics.org/index.php?title=Gene-finding&action=edit" class="new" title="Gene-finding">Gene-finding</a> </li></ul> <div class="editsection" style="float:right;margin-left:5px;">[<a href="/web/20070707152120/http://wikiomics.org/index.php?title=List_of_articles&action=edit&section=12" title="List of articles">edit</a>]</div><a name="Viruses"></a><h2> Viruses </h2> <ul><li> <a href="/web/20070707152120/http://wikiomics.org/wiki/Tools_for_annotation_and_analysis_of_viral_genomes" title="Tools for annotation and analysis of viral genomes">Tools for annotation and analysis of viral genomes</a> </li></ul> <div class="editsection" style="float:right;margin-left:5px;">[<a href="/web/20070707152120/http://wikiomics.org/index.php?title=List_of_articles&action=edit&section=13" title="List of articles">edit</a>]</div><a name="Linux"></a><h2> Linux </h2> <ul><li> <a href="/web/20070707152120/http://wikiomics.org/wiki/Specialized_Linux_distributions" title="Specialized Linux distributions">Specialized Linux distributions</a> for bioinformatics </li></ul> <div class="editsection" style="float:right;margin-left:5px;">[<a href="/web/20070707152120/http://wikiomics.org/index.php?title=List_of_articles&action=edit&section=14" title="List of articles">edit</a>]</div><a name="Bioinformatics_and_databases"></a><h2> Bioinformatics and databases </h2> <ul><li> <a href="/web/20070707152120/http://wikiomics.org/wiki/Database_downloads" title="Database downloads">Database downloads</a> </li></ul> <div class="editsection" style="float:right;margin-left:5px;">[<a href="/web/20070707152120/http://wikiomics.org/index.php?title=List_of_articles&action=edit&section=15" title="List of articles">edit</a>]</div><a name="Large-scale_and_intensive_computing"></a><h2> Large-scale and intensive computing </h2> <ul><li> <a href="/web/20070707152120/http://wikiomics.org/wiki/Grid_computing" title="Grid computing">Grid computing</a> in practice </li></ul> <div class="editsection" style="float:right;margin-left:5px;">[<a href="/web/20070707152120/http://wikiomics.org/index.php?title=List_of_articles&action=edit&section=16" title="List of articles">edit</a>]</div><a name="Communities_and_labs"></a><h2> Communities and labs </h2> <ul><li> <a href="/web/20070707152120/http://wikiomics.org/wiki/Automated_function_prediction_of_genes_and_proteins" title="Automated function prediction of genes and proteins">Automated function prediction of genes and proteins</a> </li><li> <a href="/web/20070707152120/http://wikiomics.org/wiki/Godzik_Lab" title="Godzik Lab">Godzik Lab</a> </li><li> <a href="https://web.archive.org/web/20070707152120/http://www.scientistsolutions.com/index.php?c=417" class="external text" title="http://www.scientistsolutions.com/index.php?c=417" rel="nofollow">ScientistSolutions Bioinformatics Forum</a> </li></ul> <div class="editsection" style="float:right;margin-left:5px;">[<a href="/web/20070707152120/http://wikiomics.org/index.php?title=List_of_articles&action=edit&section=17" title="List of articles">edit</a>]</div><a name="External_Medical_Reference_Links"></a><h2>External Medical Reference Links</h2> <ul><li><a href="https://web.archive.org/web/20070707152120/http://www.emedicine.com/" class="external text" title="http://www.emedicine.com/" rel="nofollow">eMedicine</a> Physician contributed medical articles and CME </li><li><a href="https://web.archive.org/web/20070707152120/http://www.kmle.com/" class="external text" title="http://www.kmle.com" rel="nofollow">KMLE Medical Dictionary</a> Medical dictionary and medical related links </li><li><a href="https://web.archive.org/web/20070707152120/http://www.nlm.nih.gov/" class="external text" title="http://www.nlm.nih.gov" rel="nofollow">NLM</a> (US National Library of Medicine, contains resources for patients and health care professionals) </li><li><a href="https://web.archive.org/web/20070707152120/http://www.webmd.com/" class="external text" title="http://www.webmd.com" rel="nofollow">WebMD</a> General comprehensive online health information </li></ul> <p><br/> </p> <div class="editsection" style="float:right;margin-left:5px;">[<a href="/web/20070707152120/http://wikiomics.org/index.php?title=List_of_articles&action=edit&section=18" title="List of articles">edit</a>]</div><a name="Wikiforum:_open_questions_and_wanted_articles"></a><h2> Wikiforum: open questions and wanted articles </h2> <p>Ask questions and build solutions collaboratively at <a href="/web/20070707152120/http://wikiomics.org/wiki/Wikiforum" title="Wikiforum">our wikiforum</a>. It is like a forum where threads would eventually evolve into clean tutorials: anyone can <b>ask questions about bioinformatics</b>. Just create a page where your specific question is asked. 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