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Finished level genomic sequences
<!DOCTYPE html> <html lang="en"> <head> <meta charset="UTF-8" /> <meta property="og:title" content="Finished level genomic sequences" /> <meta property="og:url" content="https://www.ddbj.nig.ac.jp/ddbj/finished_level_genome-e.html" /> <meta property="og:description" content="Finished level genomic sequences (non-WGS)Nucleotide sequence must meet the foll..." /> <meta property6="og:image" content="/images/thumbnail/logo_ddbj_fb.png" /> <meta name="viewport" content="width=device-width, initial-scale=1.0" /> <title>Finished level genomic sequences</title> <script async src="https://www.google-analytics.com/analytics.js"></script> <script src="https://code.jquery.com/jquery-3.5.0.js" integrity="sha256-r/AaFHrszJtwpe+tHyNi/XCfMxYpbsRg2Uqn0x3s2zc=" crossorigin="anonymous"></script> <script src="https://cdnjs.cloudflare.com/ajax/libs/jquery.hoverintent/1.10.1/jquery.hoverIntent.min.js" integrity="sha512-gx3WTM6qxahpOC/hBNUvkdZARQ2ObXSp/m+jmsEN8ZNJPymj8/Jamf8+/3kJQY1RZA2DR+KQfT+b3JEB0r9YRg==" crossorigin="anonymous"></script> <script src="https://cdnjs.cloudflare.com/ajax/libs/spin.js/4.1.0/spin.min.js" integrity="sha512-CbohqWjAgarTqRHcX1MbwkF2pujwbsCee1PABpnBWC+VqSldvlNEEI5+4OSsR/HbFQOFFpwY2YvZZNjBMxNnXg==" crossorigin="anonymous"></script> <script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/jquery.colorbox/1.6.4/jquery.colorbox-min.js"></script> <script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/jquery-deparam/0.5.3/jquery-deparam.min.js"></script> <script type="text/javascript" src="https://www.ddbj.nig.ac.jp/assets/js/jquery.trace.js"></script> <script type="text/javascript" src="https://www.ddbj.nig.ac.jp/assets/js/jquery.json_search.js"></script> <link rel="icon" href="https://www.ddbj.nig.ac.jp/assets/images/favicon_ddbj.ico"> <link rel="stylesheet" href="https://www.ddbj.nig.ac.jp/assets/css/colorbox.css" /> <link rel="stylesheet" href="https://www.ddbj.nig.ac.jp/assets/css/main.css" /> <link rel="alternate" type="application/rss+xml" title="My Site RSS" href="/feed.xml" /> <script src="https://www.ddbj.nig.ac.jp/assets/js/main.js"></script> </head> <body data-category="ddbj"> <script src="https://www.ddbj.nig.ac.jp/assets/js/ddbj_common_framework.js" id="DDBJ_common_framework" style="display: block; 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It can contain sequencing gaps. In general, finished level genomic sequences refer to the full-length sequences of the chromosome.</li> <li>Each chromosome entry must be a single contiguous sequence. Finished level genomic sequences can include organelle in eukaryotes or plasmid in prokaryotes sequences as well as chromosomes.</li> <li>Each entry comprising a genome must be assigned either a chromosome, an organelle, or a plasmid. An entry that has a missing chromosome number (e.g. unanchored) can also be included as part of the finished level genomic sequences set.</li> <li>In prokaryotes, the full length of the nucleotide sequence of a replicon (chromosome or plasmid) is expected to be submitted.</li> <li>In eukaryotes, the sequence of each chromosome that contains sequencing gaps (difficult-to-read regions such as centromeres, telomeres, and repeats) can be registered as finished level. In this entry, annotation of the sequencing gap region is required.</li> </ul> <p><br /><strong>How to submit to finished level genomic sequences and requirements</strong></p> <ul> <li>In order to submit finished level genomic sequences, please apply at the<a href="https://www.ddbj.nig.ac.jp/ddbj/mss-e.html"> Mass Submission System (MSS)</a><span style="text-decoration:underline;"> </span>.</li> <li>Registration of both<a href="https://www.ddbj.nig.ac.jp/bioproject/index-e.html">BioProject</a> and <a href="https://www.ddbj.nig.ac.jp/biosample/index-e.html">BioSample</a> are required for submission of finished level genomic sequences in advance. Description of a single accession number of BioProject and BioSample are needed on Finished level genomic sequences.</li> <li>Raw read sequences can be registered at the<a href="https://www.ddbj.nig.ac.jp/dra/index-e.html"> DDBJ Sequence Read Archive (DRA)</a>. Accession number of run data that are used to construct the assembled genome sequences should be written on entries of Finished level genomic sequences.</li> <li>If biological features such as CDS, tRNA, rRNA and so on are annotated to the sequences, application of a<a href="https://www.ddbj.nig.ac.jp/ddbj/locus_tag-e.html"> locus_tag prefix</a> for each genomes is mandatory one the submission of<a href="https://www.ddbj.nig.ac.jp/biosample/index-e.html"> BioSample Database</a>.</li> <li>If biological features such as CDS, tRNA, rRNA and so on are annotated to the sequences, registration of a<a href="https://www.ddbj.nig.ac.jp/ddbj/locus_tag-e.html"> locus_tag prefix</a> is mandatory on the submission of <a href="https://www.ddbj.nig.ac.jp/biosample/index-e.html">BioSample</a> every genomes.</li> <li>Although annotation of biological features is optional, it is required for genome sequences from species that have not been available.</li> </ul> <p>Please also visit the following web site in more detail.</p> <ul> <li><a href="https://www.ddbj.nig.ac.jp/ddbj/genome-e.html">Data submission from Genome Project</a></li> <li><a href="https://www.ddbj.nig.ac.jp/ddbj/assembly.html">INSDC standards for genome assembly submission</a></li> </ul> <p><br /><strong>Example DDBJ flat file format</strong></p> <p><strong>Aspect of Finished level genomic sequences</strong></p> <ul> <li><a href="https://www.ddbj.nig.ac.jp/ddbj/flat-file-e.html#ACCESSION">Accession number</a>; Basically, each Finished level genomic sequence submitted to DDBJ is assigned an accession number that consists of 2 alphabet characters and 6 digits .</li> <li><a href="https://www.ddbj.nig.ac.jp/ddbj/flat-file-e.html#DEFINITION">DEFINITION</a> ; The following information is displayed. <ul> <li>In the case of which entry consists of only a single chromosome in prokaryotes genome sequences, “complete genome” is shown to indicate that entry is the full length of genome sequence.</li> <li>In eukaryotes, an entry that is composed of consecutive sequences for a single chromosome shows chromosome number.</li> </ul> </li> <li><a href="https://www.ddbj.nig.ac.jp/ddbj/flat-file.html#COMMENT">COMMENT</a> block includes Genome-Assembly-Data and information related to genome assembly. Here are the tag names of Genome-Assembly-Data.</li> </ul> <table> <tr> <td> Tag name </td> <td>Value （information） </td> </tr> <tr> <td>Assembly Method </td> <td>Name of the assembly algorithm(s) with version number it was run. </td> </tr> <tr> <td>Assembly Name </td> <td>A brief name suitable for display that does not include the organism name. This is mandatory for eukaryotes. </td> </tr> <tr> <td>Genome Coverage </td> <td>The estimated base coverage across the genome. </td> </tr> <tr> <td>Sequencing Technology </td> <td>sequencing platform(s) used. </td> </tr> </table> <ul> <li>Example flat file for prokaryotes genome sequences entries <ul> <li>Accession:<a href="http://getentry.ddbj.nig.ac.jp/getentry/na/AP025277-AP025279/?format=flatfile&filetype=html&trace=true&show_suppressed=false&limit=10"> AP025277-AP025279</a></li> <li>Aeromonas hydrophila strain; NUITM-VA1, chromosome and plasmid</li> </ul> </li> <li>Example flat file for eukaryotes genome sequences entries <ul> <li>Accession:<a href="http://getentry.ddbj.nig.ac.jp/getentry/na/AP023152-AP023171/?format=flatfile&filetype=html&trace=true&show_suppressed=false&limit=10"> AP023152-AP023171</a></li> <li>Felis catus, chromosome genome assemblies</li> <li><a href="http://getentry.ddbj.nig.ac.jp/getentry/na/AP023152/?format=flatfile&filetype=html&trace=true&show_suppressed=false&limit=10">AP023152</a> chromosome A1 entry</li> </ul> </li> </ul> </main> <aside class="related-pages"> <h2 class="caption">Related pages</h2> <div class="navigation"> <nav> <ul> <li> <a href="/ddbj/genome-e.html">Data Submission from Genome Project</a> </li> <li> <a href="/ddbj/environmental-e.html">Submission of environmental sequences</a> </li> <li> <a href="/ddbj/transcriptome-e.html">Data Submission from Transcriptome Project</a> </li> <li> <a href="/ddbj/tpa-e.html">Third Party Data (TPA)</a> </li> </ul> </nav> </div> </aside> </section> </div> </section> </div> <footer></footer> <div id="back-top"></div> </body> </html>