MetabarcodingSchool/OBIJupyterHub
1
0
Fork 0
Code Issues Pull Requests 1 Actions Packages Projects Releases Wiki Activity
Files
021e2a3919965fd0c6a8aefce4a97ffb0da9d301
OBIJupyterHub/jupyterhub_volumes/web/obidoc/formats/genbank/index.html
Eric Coissac 30b7175702 Make cleaning
2025-11-17 14:18:13 +01:00

1753 lines
34 KiB
HTML
Raw Blame History

<!DOCTYPE html>
<html lang="en-us" dir="ltr">
<head>
<meta charset="UTF-8">
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<meta name="description" content="
The GenBank Flat File format
#
The
GenBank Flat File format is a widely used text-based format for storing nucleotide sequence data and their associated annotations. It is maintained by the
National Center for Biotechnology Information (NCBI) and serves as a primary repository for sequence data in the United States.
Overview
#
The GenBank format is designed to be both human-readable and machine-readable, making it suitable for manual inspection and automated processing. Each flat file contains a sequence record that includes metadata about the sequence, as well as the sequence itself. Each file can contain one or more records, with each record separated by a line containing only a // (slash-slash) string.">
<meta name="theme-color" media="(prefers-color-scheme: light)" content="#ffffff">
<meta name="theme-color" media="(prefers-color-scheme: dark)" content="#343a40">
<meta name="color-scheme" content="light dark"><meta property="og:url" content="http://metabar:8888/obidoc/formats/genbank/">
<meta property="og:site_name" content="OBITools4 documentation">
<meta property="og:title" content="GenBank Flat File format">
<meta property="og:description" content="The GenBank Flat File format # The GenBank Flat File format is a widely used text-based format for storing nucleotide sequence data and their associated annotations. It is maintained by the National Center for Biotechnology Information (NCBI) and serves as a primary repository for sequence data in the United States.
Overview # The GenBank format is designed to be both human-readable and machine-readable, making it suitable for manual inspection and automated processing. Each flat file contains a sequence record that includes metadata about the sequence, as well as the sequence itself. Each file can contain one or more records, with each record separated by a line containing only a // (slash-slash) string.">
<meta property="og:locale" content="en_us">
<meta property="og:type" content="website">
<title>GenBank Flat File format | OBITools4 documentation</title>
<link rel="icon" href="/obidoc/favicon.png" >
<link rel="manifest" href="/obidoc/manifest.json">
<link rel="canonical" href="http://metabar:8888/obidoc/formats/genbank/">
<link rel="stylesheet" href="/obidoc/book.min.5fd7b8e2d1c0ae15da279c52ff32731130386f71b58f011468f20d0056fe6b78.css" integrity="sha256-X9e44tHArhXaJ5xS/zJzETA4b3G1jwEUaPINAFb&#43;a3g=" crossorigin="anonymous">
<script defer src="/obidoc/fuse.min.js"></script>
<script defer src="/obidoc/en.search.min.4da51bdd2d833922fdbc0e19df517221387fc625ffb68ee140d605b3c5b68058.js" integrity="sha256-TaUb3S2DOSL9vA4Z31FyITh/xiX/to7hQNYFs8W2gFg=" crossorigin="anonymous"></script>
<script defer src="/obidoc/sw.min.32af8eafce4180aa1c5dea66d99fb26ba9043ea7c7a4c706138c91d9051b285e.js" integrity="sha256-Mq&#43;Or85BgKocXepm2Z&#43;ya6kEPqfHpMcGE4yR2QUbKF4=" crossorigin="anonymous"></script>
<link rel="alternate" type="application/rss+xml" href="http://metabar:8888/obidoc/formats/genbank/index.xml" title="OBITools4 documentation" />
<!--
Made with Book Theme
https://github.com/alex-shpak/hugo-book
-->
<link rel="stylesheet" type="text/css" href="http://metabar:8888/obidoc/hugo-cite.css" />
</head>
<body dir="ltr">
<input type="checkbox" class="hidden toggle" id="menu-control" />
<input type="checkbox" class="hidden toggle" id="toc-control" />
<main class="container flex">
<aside class="book-menu">
<div class="book-menu-content">
<nav>
<h2 class="book-brand">
<a class="flex align-center" href="/obidoc/"><img src="/obidoc/obitools_logo.jpg" alt="Logo" class="book-icon" /><span>OBITools4 documentation</span>
</a>
</h2>
<div class="book-search hidden">
<input type="text" id="book-search-input" placeholder="Search" aria-label="Search" maxlength="64" data-hotkeys="s/" />
<div class="book-search-spinner hidden"></div>
<ul id="book-search-results"></ul>
</div>
<script>document.querySelector(".book-search").classList.remove("hidden")</script>
<ul>
<li>
<span>Docs</span>
<ul>
<li>
<a href="/obidoc/docs/about/" class="">About</a>
</li>
<li>
<a href="/obidoc/docs/installation/" class="">Installation</a>
<ul>
</ul>
</li>
<li>
<a href="/obidoc/docs/principles/" class="">General operating principles</a>
<ul>
</ul>
</li>
<li>
<input type="checkbox" id="section-08756b4c1f14be6ee584ece005b9f621" class="toggle" checked />
<label for="section-08756b4c1f14be6ee584ece005b9f621" class="flex justify-between">
<a role="button" class="">File formats</a>
</label>
<ul>
<li>
<input type="checkbox" id="section-933c2e64b905b84e22aa5273cea2d0bd" class="toggle" checked />
<label for="section-933c2e64b905b84e22aa5273cea2d0bd" class="flex justify-between">
<a role="button" class="">Sequence file formats</a>
</label>
<ul>
<li>
<a href="/obidoc/formats/fasta/" class="">FASTA file format</a>
<ul>
</ul>
</li>
<li>
<a href="/obidoc/formats/fastq/" class="">FASTQ file format</a>
<ul>
</ul>
</li>
<li>
<a href="/obidoc/formats/genbank/" class="active">GenBank Flat File format</a>
<ul>
</ul>
</li>
<li>
<a href="/obidoc/formats/embl/" class="">EMBL Flat File format</a>
<ul>
</ul>
</li>
<li>
<a href="/obidoc/docs/file_format/sequence_files/csv/" class="">CSV format</a>
<ul>
</ul>
</li>
<li>
<a href="/obidoc/formats/json/" class="">JSON format</a>
<ul>
</ul>
</li>
<li>
<a href="/obidoc/docs/file_format/sequence_files/annotations/" class="">Annotation of sequences</a>
<ul>
</ul>
</li>
</ul>
</li>
<li>
<input type="checkbox" id="section-0258ae1c222f9a38cc1b75254c93b0f4" class="toggle" />
<label for="section-0258ae1c222f9a38cc1b75254c93b0f4" class="flex justify-between">
<a role="button" class="">Taxonomy file formats</a>
</label>
<ul>
<li>
<a href="/obidoc/docs/file_format/taxonomy_file/csv_taxdump/" class="">CSV formatted taxdump</a>
<ul>
</ul>
</li>
<li>
<a href="/obidoc/docs/file_format/taxonomy_file/ncbi_taxdump/" class="">NCBI taxdump</a>
<ul>
</ul>
</li>
</ul>
</li>
<li>
<a href="/obidoc/formats/csv/" class="">The CSV format</a>
<ul>
</ul>
</li>
</ul>
</li>
<li>
<input type="checkbox" id="section-70b1e6e5ec7f3ccab643155fa50659b6" class="toggle" />
<label for="section-70b1e6e5ec7f3ccab643155fa50659b6" class="flex justify-between">
<a role="button" class="">Patterns</a>
</label>
<ul>
<li>
<a href="/obidoc/docs/patterns/regular/" class="">Regular Expressions</a>
</li>
<li>
<a href="/obidoc/docs/patterns/dnagrep/" class="">DNA Patterns</a>
</li>
</ul>
</li>
<li>
<input type="checkbox" id="section-8223f464911a1fe6c655972143684e93" class="toggle" />
<label for="section-8223f464911a1fe6c655972143684e93" class="flex justify-between">
<a role="button" class="">The OBITools4 commands</a>
</label>
<ul>
<li>
<a href="/obidoc/docs/commands/options/" class="">Shared command options</a>
<ul>
</ul>
</li>
<li>
<input type="checkbox" id="section-8921ea65523c266b128dd4263232b0fc" class="toggle" />
<label for="section-8921ea65523c266b128dd4263232b0fc" class="flex justify-between">
<a role="button" class="">Basics</a>
</label>
<ul>
<li>
<a href="/obidoc/obitools/obiannotate/" class="">obiannotate</a>
<ul>
</ul>
</li>
<li>
<a href="/obidoc/obitools/obicomplement/" class="">obicomplement</a>
<ul>
</ul>
</li>
<li>
<a href="/obidoc/obitools/obiconvert/" class="">obiconvert</a>
<ul>
</ul>
</li>
<li>
<a href="/obidoc/obitools/obicount/" class="">obicount</a>
<ul>
</ul>
</li>
<li>
<a href="/obidoc/obitools/obicsv/" class="">obicsv</a>
<ul>
</ul>
</li>
<li>
<a href="/obidoc/obitools/obidemerge/" class="">obidemerge</a>
<ul>
</ul>
</li>
<li>
<a href="/obidoc/obitools/obidistribute/" class="">obidistribute</a>
<ul>
</ul>
</li>
<li>
<a href="/obidoc/obitools/obigrep/" class="">obigrep</a>
<ul>
</ul>
</li>
<li>
<a href="/obidoc/obitools/obijoin/" class="">obijoin</a>
<ul>
</ul>
</li>
<li>
<a href="/obidoc/obitools/obimatrix/" class="">obimatrix</a>
<ul>
</ul>
</li>
<li>
<a href="/obidoc/obitools/obisplit/" class="">obisplit</a>
<ul>
</ul>
</li>
<li>
<a href="/obidoc/obitools/obisummary/" class="">obisummary</a>
<ul>
</ul>
</li>
<li>
<a href="/obidoc/obitools/obiuniq/" class="">obiuniq</a>
<ul>
</ul>
</li>
</ul>
</li>
<li>
<input type="checkbox" id="section-dbdf1bb5377572439394e60e08c30f50" class="toggle" />
<label for="section-dbdf1bb5377572439394e60e08c30f50" class="flex justify-between">
<a role="button" class="">Demultiplexing samples</a>
</label>
<ul>
<li>
<a href="/obidoc/obitools/obimultiplex/" class="">obimultiplex</a>
<ul>
</ul>
</li>
<li>
<a href="/obidoc/obitools/obitagpcr/" class="">obitagpcr</a>
<ul>
</ul>
</li>
</ul>
</li>
<li>
<input type="checkbox" id="section-aa98fedd067b51150db59691a8ea8edd" class="toggle" />
<label for="section-aa98fedd067b51150db59691a8ea8edd" class="flex justify-between">
<a role="button" class="">Sequence alignments</a>
</label>
<ul>
<li>
<a href="/obidoc/obitools/obiclean/" class="">obiclean</a>
<ul>
</ul>
</li>
<li>
<input type="checkbox" id="section-7433746525d8c2b29b033f765c869acd" class="toggle" />
<label for="section-7433746525d8c2b29b033f765c869acd" class="flex justify-between">
<a href="/obidoc/obitools/obipairing/" class="">obipairing</a>
</label>
<ul>
<li>
<a href="/obidoc/docs/commands/alignments/obipairing/fasta-like/" class="">The FASTA-like alignment</a>
<ul>
</ul>
</li>
<li>
<a href="/obidoc/docs/commands/alignments/obipairing/exact-alignment/" class="">Exact alignment</a>
<ul>
</ul>
</li>
</ul>
</li>
<li>
<a href="/obidoc/obitools/obipcr/" class="">obipcr</a>
<ul>
</ul>
</li>
<li>
<a href="/obidoc/obitools/obirefidx/" class="">obirefidx</a>
<ul>
</ul>
</li>
<li>
<a href="/obidoc/obitools/obitag/" class="">obitag</a>
<ul>
</ul>
</li>
</ul>
</li>
<li>
<input type="checkbox" id="section-5746f699d10490780dec8e30ab2dd3ce" class="toggle" />
<label for="section-5746f699d10490780dec8e30ab2dd3ce" class="flex justify-between">
<a role="button" class="">Taxonomy</a>
</label>
<ul>
<li>
<a href="/obidoc/obitools/obitaxonomy/" class="">obitaxonomy</a>
<ul>
</ul>
</li>
</ul>
</li>
<li>
<input type="checkbox" id="section-3f50c4fe7ab436a56ae92897d5444956" class="toggle" />
<label for="section-3f50c4fe7ab436a56ae92897d5444956" class="flex justify-between">
<a role="button" class="">Advanced tools</a>
</label>
<ul>
<li>
<a href="/obidoc/obitools/obiscript/" class="">obiscript</a>
<ul>
</ul>
</li>
</ul>
</li>
<li>
<input type="checkbox" id="section-549be3934679fcb82a232f6bd5435563" class="toggle" />
<label for="section-549be3934679fcb82a232f6bd5435563" class="flex justify-between">
<a role="button" class="">Others</a>
</label>
<ul>
<li>
<a href="/obidoc/obitools/obimicrosat/" class="">obimicrosat</a>
<ul>
</ul>
</li>
</ul>
</li>
<li>
<input type="checkbox" id="section-ceca4455173761e30cbc0a6dc2327167" class="toggle" />
<label for="section-ceca4455173761e30cbc0a6dc2327167" class="flex justify-between">
<a role="button" class="">Experimentals</a>
</label>
<ul>
<li>
<a href="/obidoc/obitools/obicleandb/" class="">obicleandb</a>
<ul>
</ul>
</li>
<li>
<a href="/obidoc/obitools/obiconsensus/" class="">obiconsensus</a>
<ul>
</ul>
</li>
<li>
<a href="/obidoc/obitools/obilandmark/" class="">obilandmark</a>
<ul>
</ul>
</li>
</ul>
</li>
<li>
<a href="/obidoc/docs/commands/tags/" class="">Glossary of tags</a>
</li>
</ul>
</li>
<li>
<input type="checkbox" id="section-9b1bcd52530c59dc4819b1f61c128f54" class="toggle" />
<label for="section-9b1bcd52530c59dc4819b1f61c128f54" class="flex justify-between">
<a role="button" class="">Cookbook</a>
</label>
<ul>
<li>
<a href="/obidoc/docs/cookbook/illumina/" class="">Analysing an Illumina data set</a>
<ul>
</ul>
</li>
<li>
<a href="/obidoc/docs/cookbook/ecoprimers/" class="">Designing new barcodes</a>
<ul>
</ul>
</li>
<li>
<a href="/obidoc/docs/cookbook/local_genbank/" class="">Prepare a local copy of Genbank</a>
<ul>
</ul>
</li>
<li>
<a href="/obidoc/docs/cookbook/reference_db/" class="">Build a reference database</a>
<ul>
</ul>
</li>
<li>
<a href="/obidoc/docs/cookbook/minion/" class="">Oxford Nanopore data analysis</a>
<ul>
</ul>
</li>
</ul>
</li>
<li>
<span>Programming OBITools</span>
<ul>
<li>
<a href="/obidoc/docs/programming/expression/" class="">Expression language</a>
<ul>
</ul>
</li>
<li>
<input type="checkbox" id="section-6d580829a667b5cca790b286d99a10fe" class="toggle" />
<label for="section-6d580829a667b5cca790b286d99a10fe" class="flex justify-between">
<a href="/obidoc/docs/programming/lua/" class="">Lua: for scripting OBITools</a>
</label>
<ul>
<li>
<input type="checkbox" id="section-2fb081dac812d624eea5f4268fca9e26" class="toggle" />
<label for="section-2fb081dac812d624eea5f4268fca9e26" class="flex justify-between">
<a role="button" class="">Obitools Classes</a>
</label>
<ul>
<li>
<a href="/obidoc/docs/programming/lua/obitools_classes/biosequence/" class="">BioSequence</a>
<ul>
</ul>
</li>
<li>
<a href="/obidoc/docs/programming/lua/obitools_classes/biosequenceslice/" class="">BioSequenceSlice</a>
<ul>
</ul>
</li>
<li>
<a href="/obidoc/docs/programming/lua/obitools_classes/taxonomy/" class="">Taxonomy</a>
<ul>
</ul>
</li>
<li>
<a href="/obidoc/docs/programming/lua/obitools_classes/taxon/" class="">Taxon</a>
<ul>
</ul>
</li>
<li>
<a href="/obidoc/docs/programming/lua/obitools_classes/mutex/" class="">Mutex</a>
<ul>
</ul>
</li>
</ul>
</li>
</ul>
</li>
</ul>
</li>
</ul>
</li>
</ul>
</nav>
<script>(function(){var e=document.querySelector("aside .book-menu-content");addEventListener("beforeunload",function(){localStorage.setItem("menu.scrollTop",e.scrollTop)}),e.scrollTop=localStorage.getItem("menu.scrollTop")})()</script>
</div>
</aside>
<div class="book-page">
<header class="book-header">
<div class="flex align-center justify-between">
<label for="menu-control">
<img src="/obidoc/svg/menu.svg" class="book-icon" alt="Menu" />
</label>
<h3>GenBank Flat File format</h3>
<label for="toc-control">
<img src="/obidoc/svg/toc.svg" class="book-icon" alt="Table of Contents" />
</label>
</div>
<aside class="hidden clearfix">
<nav id="TableOfContents">
<ul>
<li><a href="#the-genbank-flat-file-format">The <em>GenBank</em> Flat File format</a>
<ul>
<li><a href="#overview">Overview</a></li>
<li><a href="#structure-of-the-genbank-flat-file-record">Structure of the GenBank Flat File record</a>
<ul>
<li><a href="#header-section">Header section</a></li>
<li><a href="#feature-table-section">Feature table section</a></li>
<li><a href="#sequence-section">Sequence section</a></li>
<li><a href="#terminator">Terminator</a></li>
</ul>
</li>
<li><a href="#converting-genbank-flat-file-to-fasta-format">Converting GenBank Flat File to FASTA format</a></li>
<li><a href="#references">References</a></li>
</ul>
</li>
</ul>
</nav>
</aside>
</header>
<article class="markdown book-article"><h1 id="the-genbank-flat-file-format">
The <em>GenBank</em> Flat File format
<a class="anchor" href="#the-genbank-flat-file-format">#</a>
</h1>
<p>The
<a href="https://www.ncbi.nlm.nih.gov/genbank/samplerecord/">GenBank Flat File format</a> is a widely used text-based format for storing nucleotide sequence data and their associated annotations. It is maintained by the
<a href="https://www.ncbi.nlm.nih.gov/">National Center for Biotechnology Information (NCBI)</a> and serves as a primary repository for sequence data in the United States.</p>
<h2 id="overview">
Overview
<a class="anchor" href="#overview">#</a>
</h2>
<p>The GenBank format is designed to be both human-readable and machine-readable, making it suitable for manual inspection and automated processing. Each flat file contains a sequence record that includes metadata about the sequence, as well as the sequence itself. Each file can contain one or more records, with each record separated by a line containing only a <code>//</code> (slash-slash) string.</p>
<p><a style="padding: 10px 20px; background-color: #cacaca; border: 1px solid #8e8080; border-bottom: none; border-radius: 5px 5px 0 0; box-shadow: 0 2px 5px rgba(0, 0, 0, 0.1)"
href="sample.gb" download="sample.gb">📄 sample.gb</a></p>
<DIV style="border: 2px solid #8e8080; border-radius: 0 0 5px 5px; padding: 20px; background-color: white; ">
<pre tabindex="0"><code class="language-genbank" data-lang="genbank">LOCUS HQ324066 84 bp DNA linear PLN 18-NOV-2011
DEFINITION Trinia glauca tRNA-Leu (trnL) gene, intron; chloroplast.
ACCESSION HQ324066
VERSION HQ324066.1
KEYWORDS .
SOURCE chloroplast Trinia glauca
ORGANISM Trinia glauca
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
Spermatophyta; Magnoliopsida; eudicotyledons; Gunneridae;
Pentapetalae; asterids; campanulids; Apiales; Apiaceae; Apioideae;
apioid superclade; Selineae; Trinia.
REFERENCE 1 (bases 1 to 84)
AUTHORS Raye,G., Miquel,C., Coissac,E., Redjadj,C., Loison,A. and
Taberlet,P.
TITLE New insights on diet variability revealed by DNA barcoding and
high-throughput pyrosequencing: chamois diet in autumn as a case
study
JOURNAL Ecol. Res. 26 (2), 265-276 (2011)
REFERENCE 2 (bases 1 to 84)
AUTHORS Raye,G.
TITLE Direct Submission
JOURNAL Submitted (25-SEP-2010) LECA, Universite Joseph Fourier, Bp 53,
2233 rue de la Piscine, Grenoble 38041, France
FEATURES Location/Qualifiers
source 1..84
/organism=&#34;Trinia glauca&#34;
/organelle=&#34;plastid:chloroplast&#34;
/mol_type=&#34;genomic DNA&#34;
/db_xref=&#34;taxon:1000432&#34;
/geo_loc_name=&#34;France&#34;
gene &lt;1..&gt;84
/gene=&#34;trnL&#34;
/note=&#34;tRNA-Leu; tRNA-Leu(UAA)&#34;
intron &lt;1..&gt;84
/gene=&#34;trnL&#34;
/note=&#34;P6 loop&#34;
ORIGIN
1 gggcaatcct gagccaaatc ctattttaca aaaacaaaca aaggcccaga aggtgaaaaa
61 aggataggtg cagagactca atgg
//
</code></pre></td>
</DIV>
<h2 id="structure-of-the-genbank-flat-file-record">
Structure of the GenBank Flat File record
<a class="anchor" href="#structure-of-the-genbank-flat-file-record">#</a>
</h2>
<p>A GenBank flat file consists of several sections, each containing specific information about the sequence. The main sections include:</p>
<h3 id="header-section">
Header section
<a class="anchor" href="#header-section">#</a>
</h3>
<p>The header section contains essential metadata about the sequence. The following fields are commonly found in this section:</p>
<ul>
<li><strong>LOCUS</strong>: A unique identifier for the sequence, including its length, type (<em>e.g.</em>, DNA, RNA), and whether it is linear or circular.</li>
<li><strong>DEFINITION</strong>: A brief description of the sequence, summarizing its biological significance.</li>
<li><strong>ACCESSION</strong>: Accession number(s) associated with the sequence, which can be used to retrieve the record.</li>
<li><strong>VERSION</strong>: The version number of the sequence record, indicating updates or changes.</li>
<li><strong>KEYWORDS</strong>: Keywords associated with the sequence, making it easier to categorise and search.</li>
<li><strong>SOURCE</strong>: The organism from which the sequence is derived, including the scientific name.</li>
<li><strong>REFERENCE</strong>: Citations for the sequence, linking it to relevant literature.</li>
</ul>
<pre tabindex="0"><code>LOCUS HQ324066 84 bp DNA linear PLN 18-NOV-2011
DEFINITION Trinia glauca tRNA-Leu (trnL) gene, intron; chloroplast.
ACCESSION HQ324066
VERSION HQ324066.1
KEYWORDS .
SOURCE chloroplast Trinia glauca
ORGANISM Trinia glauca
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
Spermatophyta; Magnoliopsida; eudicotyledons; Gunneridae;
Pentapetalae; asterids; campanulids; Apiales; Apiaceae; Apioideae;
apioid superclade; Selineae; Trinia.
REFERENCE 1 (bases 1 to 84)
AUTHORS Raye,G., Miquel,C., Coissac,E., Redjadj,C., Loison,A. and
Taberlet,P.
TITLE New insights on diet variability revealed by DNA barcoding and
high-throughput pyrosequencing: chamois diet in autumn as a case
study
JOURNAL Ecol. Res. 26 (2), 265-276 (2011)
REFERENCE 2 (bases 1 to 84)
AUTHORS Raye,G.
TITLE Direct Submission
JOURNAL Submitted (25-SEP-2010) LECA, Universite Joseph Fourier, Bp 53,
2233 rue de la Piscine, Grenoble 38041, France
</code></pre><h3 id="feature-table-section">
Feature table section
<a class="anchor" href="#feature-table-section">#</a>
</h3>
<p>The feature table section contains information about the annotations or features of the sequence, such as genes, transcripts, or regions. Each feature is represented by a set of fields splitted over multiple lines. The first line of each feature contains the feature type, such as &ldquo;gene&rdquo;, &ldquo;transcript&rdquo;, or &ldquo;region&rdquo; and its location in the sequence. The subsequent lines contain the feature-specific information, such as the gene name, gene function, cross-references to other databases, or its translation to protein for protein-coding genes.</p>
<pre tabindex="0"><code>FEATURES Location/Qualifiers
source 1..84
/organism=&#34;Trinia glauca&#34;
/organelle=&#34;plastid:chloroplast&#34;
/mol_type=&#34;genomic DNA&#34;
/db_xref=&#34;taxon:1000432&#34;
/geo_loc_name=&#34;France&#34;
gene &lt;1..&gt;84
/gene=&#34;trnL&#34;
/note=&#34;tRNA-Leu; tRNA-Leu(UAA)&#34;
intron &lt;1..&gt;84
/gene=&#34;trnL&#34;
/note=&#34;P6 loop&#34;
</code></pre><h3 id="sequence-section">
Sequence section
<a class="anchor" href="#sequence-section">#</a>
</h3>
<p>The sequence section contains the sequence data itself, starting with a line containing only the keyword <code>ORIGIN</code> (in uppercase), followed by the sequence data. The sequence data is separated by spaces every 10 characters and each line contains 60 nucleotides. The number on the left of each sequence lines indicates the start position of the line in the sequence.</p>
<pre tabindex="0"><code>ORIGIN
1 gggcaatcct gagccaaatc ctattttaca aaaacaaaca aaggcccaga aggtgaaaaa
61 aggataggtg cagagactca atgg
</code></pre><h3 id="terminator">
Terminator
<a class="anchor" href="#terminator">#</a>
</h3>
<p>The record concludes with a <code>//</code> line, indicating the end of the record. This terminator is crucial for distinguishing between multiple records in a single file.</p>
<pre tabindex="0"><code>//
</code></pre><h2 id="converting-genbank-flat-file-to-fasta-format">
Converting GenBank Flat File to FASTA format
<a class="anchor" href="#converting-genbank-flat-file-to-fasta-format">#</a>
</h2>
<p>To convert a GenBank flat file to
<a href="http://metabar:8888/obidoc/formats/fasta/">fasta</a>
format, you can use the <a href="http://metabar:8888/obidoc/obitools/obiconvert/">
<abbr title="obiconvert: convert format of a sequence file"><code>obiconvert</code></abbr>
</a> command.
The <a href="http://metabar:8888/obidoc/obitools/obiconvert/">
<abbr title="obiconvert: convert format of a sequence file"><code>obiconvert</code></abbr>
</a> command extracts the taxid and scientific name associated with each GenBank record and stores them in the <code>taxid</code> and <code>scientific_name</code> tags in the FASTA header.</p>
<div class="highlight"><pre tabindex="0" style="color:#f8f8f2;background-color:#272822;-moz-tab-size:4;-o-tab-size:4;tab-size:4;"><code class="language-bash" data-lang="bash"><span style="display:flex;"><span>obiconvert sample.gb
</span></span></code></pre></div><pre tabindex="0"><code class="language-fasta" data-lang="fasta">&gt;HQ324066 {&#34;definition&#34;:&#34;Trinia glauca tRNA-Leu (trnL) gene, intron; chloroplast.&#34;,&#34;scientific_name&#34;:&#34;chloroplast Trinia glauca&#34;,&#34;taxid&#34;:1000432}
gggcaatcctgagccaaatcctattttacaaaaacaaacaaaggcccagaaggtgaaaaa
aggataggtgcagagactcaatgg
</code></pre></td>
<link rel="stylesheet" href="/obidoc/css/vendors/admonitions.5c73bad2903e7d2d44ad118370ebd8c2cf5f239d4d93c283e55c00f2f8d30746.css" integrity="sha256-XHO60pA&#43;fS1ErRGDcOvYws9fI51Nk8KD5VwA8vjTB0Y=" crossorigin="anonymous">
<div class="admonition note">
<div class="admonition-header"><svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 576 512"><path d="M0 64C0 28.7 28.7 0 64 0L224 0l0 128c0 17.7 14.3 32 32 32l128 0 0 125.7-86.8 86.8c-10.3 10.3-17.5 23.1-21 37.2l-18.7 74.9c-2.3 9.2-1.8 18.8 1.3 27.5L64 512c-35.3 0-64-28.7-64-64L0 64zm384 64l-128 0L256 0 384 128zM549.8 235.7l14.4 14.4c15.6 15.6 15.6 40.9 0 56.6l-29.4 29.4-71-71 29.4-29.4c15.6-15.6 40.9-15.6 56.6 0zM311.9 417L441.1 287.8l71 71L382.9 487.9c-4.1 4.1-9.2 7-14.9 8.4l-60.1 15c-5.5 1.4-11.2-.2-15.2-4.2s-5.6-9.7-4.2-15.2l15-60.1c1.4-5.6 4.3-10.8 8.4-14.9z"/></svg>
<span>Note</span>
</div>
<div class="admonition-content">
<p>The DDBJ database uses a format very similar to GenBank, so <a href="http://metabar:8888/obidoc/obitools/obiconvert/">
<abbr title="obiconvert: convert format of a sequence file"><code>obiconvert</code></abbr>
</a>
recognizes it as a GenBank file and correctly converts it to FASTA.</p>
</div>
</div><h2 id="references">
References
<a class="anchor" href="#references">#</a>
</h2>
<p>For more detailed specifications and guidelines regarding the GenBank Flat File format, refer to the following resource:</p>
<ul>
<li>
<a href="https://www.ncbi.nlm.nih.gov/genbank/samplerecord/">GenBank Flat File format</a></li>
</ul>
</article>
<footer class="book-footer">
<div class="flex flex-wrap justify-between">
</div>
<script>(function(){function e(e){const t=window.getSelection(),n=document.createRange();n.selectNodeContents(e),t.removeAllRanges(),t.addRange(n)}document.querySelectorAll("pre code").forEach(t=>{t.addEventListener("click",function(){if(window.getSelection().toString())return;e(t.parentElement),navigator.clipboard&&navigator.clipboard.writeText(t.parentElement.textContent)})})})()</script>
</footer>
<div class="book-comments">
</div>
<label for="menu-control" class="hidden book-menu-overlay"></label>
</div>
<aside class="book-toc">
<div class="book-toc-content">
<nav id="TableOfContents">
<ul>
<li><a href="#the-genbank-flat-file-format">The <em>GenBank</em> Flat File format</a>
<ul>
<li><a href="#overview">Overview</a></li>
<li><a href="#structure-of-the-genbank-flat-file-record">Structure of the GenBank Flat File record</a>
<ul>
<li><a href="#header-section">Header section</a></li>
<li><a href="#feature-table-section">Feature table section</a></li>
<li><a href="#sequence-section">Sequence section</a></li>
<li><a href="#terminator">Terminator</a></li>
</ul>
</li>
<li><a href="#converting-genbank-flat-file-to-fasta-format">Converting GenBank Flat File to FASTA format</a></li>
<li><a href="#references">References</a></li>
</ul>
</li>
</ul>
</nav>
</div>
</aside>
</main>
</body>
</html>
Reference in New Issue View Git Blame Copy Permalink