714 lines
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<div class="res_logo"><h1 class="img_logo"><a href="/" title="NCBI home">NCBI</a></h1><h2 class="res_tagline">National Center for Biotechnology Information</h2></div>
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<div class="search"><form method="get" action="/gquery/"><div class="search_form"><label for="database" class="offscreen_noflow">Search database</label><select id="database"><optgroup label="Recent"><option value="gquery" selected="selected">All Databases</option><option value="nuccore">Nucleotide</option><option value="clinvar">ClinVar</option><option value="gene" class="last">Gene</option></optgroup><optgroup label="All"><option value="gquery">All Databases</option><option value="assembly">Assembly</option><option value="biocollections">Biocollections</option><option value="bioproject">BioProject</option><option value="biosample">BioSample</option><option value="books">Books</option><option value="clinvar">ClinVar</option><option value="cdd">Conserved Domains</option><option value="gap">dbGaP</option><option value="dbvar">dbVar</option><option value="gene">Gene</option><option value="genome">Genome</option><option value="gds">GEO DataSets</option><option value="geoprofiles">GEO Profiles</option><option value="gtr">GTR</option><option value="ipg">Identical Protein Groups</option><option value="medgen">MedGen</option><option value="mesh">MeSH</option><option value="nlmcatalog">NLM Catalog</option><option value="nuccore">Nucleotide</option><option value="omim">OMIM</option><option value="pmc">PMC</option><option value="protein">Protein</option><option value="proteinclusters">Protein Clusters</option><option value="protfam">Protein Family Models</option><option value="pcassay">PubChem BioAssay</option><option value="pccompound">PubChem Compound</option><option value="pcsubstance">PubChem Substance</option><option value="pubmed">PubMed</option><option value="snp">SNP</option><option value="sra">SRA</option><option value="structure">Structure</option><option value="taxonomy">Taxonomy</option><option value="toolkit">ToolKit</option><option value="toolkitall">ToolKitAll</option><option value="toolkitbookgh">ToolKitBookgh</option></optgroup></select><div class="nowrap"><label for="term" class="offscreen_noflow" accesskey="/">Search term</label><div class="nowrap"><input type="text" name="term" id="term" title="Search All Databases" value="" class="jig-ncbiclearbutton jig-ncbiautocomplete" data-jigconfig="isEnabled:false,disableUrl:'NcbiSearchBarAutoComplCtrl'" autocomplete="off" data-sbconfig="ds:'no',pjs:'no',afs:'yes'" /></div><button id="search" type="submit" class="button_search nowrap" cmd="go">Search</button></div></div></form></div>
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<div id="maincontent" class="content col twelve_col last">
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<div class="col1">
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<div class="col1inner">
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<h2>How to: Submit sequence data to NCBI</h2>
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<div>
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<script>
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window.location.href = "https://submit.ncbi.nlm.nih.gov/";
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</script>
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<table border="0" cellpadding="0" id="submit-sequence-data" style="border-collapse: collapse; width: 100%;">
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<thead>
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<tr>
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<th style="border-bottom: 1px solid rgb(204, 204, 204); font-weight: normal; width: 24%; text-align: left;">
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<p>
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Starting with...</p>
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</th>
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<th style="border-bottom: 1px solid rgb(204, 204, 204); font-weight: normal; width: 52%; text-align: left;">
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<p>
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NOTES</p>
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</th>
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<th style="border-bottom: 1px solid rgb(204, 204, 204); font-weight: normal; width: 24%; text-align: center;">
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<p>
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SUBMISSION TOOLS<br />
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& HELP DOCUMENTS</p>
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</th>
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</tr>
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</thead>
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<tbody>
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<tr style="border-bottom: 1px solid rgb(229, 229, 229);">
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<td style="padding: 2px; width: 24%; background-color: rgb(255, 255, 255);">
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</td>
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<td style="padding: 2px; width: 52%; text-align: center; background-color: rgb(255, 255, 255);">
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<p align="center">
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<strong>Simple Sequence Submissions</strong>
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</p>
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</td>
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<td style="padding: 2px; width: 24%; background-color: rgb(255, 255, 255);">
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</td>
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</tr>
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<tr>
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<td style="padding: 2px; width: 24%; border-bottom: 1px solid rgb(204, 204, 204);">
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<p>
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Single nucleotide sequence</p>
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<p>
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<em>or</em>
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</p>
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<p>
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Several nucleotide sequences for <em>different</em> genes or loci</p>
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</td>
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<td style="padding: 2px; width: 52%; border-bottom: 1px solid rgb(204, 204, 204);">
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<p>
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Contiguous bases of cDNA or genomic DNA, but should not be complete genomes. Complete genomes should be submitted via the appropriate protocol indicated below.</p>
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<p>
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Records with simple annotation may be submitted by <a href="https://www.ncbi.nlm.nih.gov/WebSub/?tool=genbank">BankIt</a> or <a href="https://www.ncbi.nlm.nih.gov/Sequin/index.html">Sequin</a>, while records with complicated annotation may be more easily submitted via <a href="https://www.ncbi.nlm.nih.gov/Sequin/index.html">Sequin</a>.</p>
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</td>
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<td style="padding: 2px; width: 24%; border-bottom: 1px solid rgb(204, 204, 204);">
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<p align="center"><a href="https://www.ncbi.nlm.nih.gov/WebSub/?tool=genbank">BankIt</a> or <a href="https://www.ncbi.nlm.nih.gov/Sequin/index.html">Sequin</a></p>
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</td>
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</tr>
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<tr>
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<td style="padding: 2px; width: 24%; border-bottom: 1px solid rgb(204, 204, 204);">
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<p>
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Group of nucleotide sequences for the <em>same</em> gene or locus</p>
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</td>
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<td style="padding: 2px; width: 52%; border-bottom: 1px solid rgb(204, 204, 204);">
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<p>
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Includes:</p>
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<ul>
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<li>
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population studies (sequences for a single organism)</li>
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<li>
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phylogenetic studies (sequences for multiple organisms)</li>
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<li>
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environmental samples (such as cultured or uncultured bacteria or metagenomic samples)</li>
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</ul>
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</td>
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<td style="padding: 2px; width: 24%; border-bottom: 1px solid rgb(204, 204, 204);">
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<p align="center"><a href="https://www.ncbi.nlm.nih.gov/WebSub/?tool=genbank">BankIt</a> or <a href="https://www.ncbi.nlm.nih.gov/Sequin/index.html">Sequin</a></p>
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</td>
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||
</tr>
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<tr>
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<td style="padding: 2px; width: 24%; border-bottom: 1px solid rgb(204, 204, 204);">
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<p>
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Batches of Sequences</p>
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</td>
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<td style="padding: 2px; width: 52%; border-bottom: 1px solid rgb(204, 204, 204);">
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<p>
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Includes:</p>
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<ul>
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<li>
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Expressed Sequence Tags (ESTs)</li>
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<li>
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<span style="background-color: transparent;">Genome Survey Sequences (GSSs)</span>
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</li>
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</ul>
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</td>
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<td style="padding: 2px; width: 24%; border-bottom: 1px solid rgb(204, 204, 204);">
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<p align="center">
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<a href="https://www.ncbi.nlm.nih.gov/genbank/submit.html#ref12">Batch submit guidance page</a>
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</p>
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</td>
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</tr>
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<tr style="border-bottom: 1px solid rgb(229, 229, 229);">
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<td style="padding: 2px; width: 24%; background-color: rgb(255, 255, 255);">
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</td>
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<td style="padding: 2px; width: 52%; text-align: center; background-color: rgb(255, 255, 255);">
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<p align="center">
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||
<strong>Genomic Assembly Submissions</strong>
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</p>
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</td>
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<td style="padding: 2px; width: 24%; background-color: rgb(255, 255, 255);">
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</td>
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</tr>
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<tr>
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<td style="padding: 2px; width: 24%; border-bottom: 1px solid rgb(204, 204, 204);">
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<p>
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Small complete genomes</p>
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</td>
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<td style="padding: 2px; width: 52%; border-bottom: 1px solid rgb(204, 204, 204);">
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<p>
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Includes chloroplasts, mitochondria, plasmids, phages, and viruses<br />
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<em>(Locus_tag or BioProject registration is NOT required.)</em></p>
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</td>
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<td style="padding: 2px; width: 24%; border-bottom: 1px solid rgb(204, 204, 204);">
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<p align="center">
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||
<a href="https://www.ncbi.nlm.nih.gov/Sequin/index.html">Sequin</a>
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</p>
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</td>
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||
</tr>
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<tr>
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<td style="padding: 2px; width: 24%; height: 78px; border-bottom: 1px solid rgb(204, 204, 204);">
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<p>
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Large complete genomes</p>
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</td>
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<td style="padding: 2px; width: 52%; height: 78px; border-bottom: 1px solid rgb(204, 204, 204);">
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<p>
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Includes paired chromosome and plasmids, as well as bacterial or eukaryotic chromosomes</p>
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<p>
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Questions regarding a specific submission that are not answered in the documented instructions can be sent to <a href="mailto:genomes@ncbi.nlm.nih.gov">genomes@ncbi.nlm.nih.gov</a> .</p>
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</td>
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<td style="padding: 2px; width: 24%; height: 78px; border-bottom: 1px solid rgb(204, 204, 204);">
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<p align="center">
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<a href="https://www.ncbi.nlm.nih.gov/genbank/genomesubmit.html">Prokaryotic Genomes submission</a>
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</p>
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<p align="center">
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<a href="https://www.ncbi.nlm.nih.gov/genbank/eukaryotic_genome_submission.html">Eukaryotic Genomes submission</a>
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</p>
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</td>
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</tr>
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<tr>
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<td style="padding: 2px; width: 24%; border-bottom: 1px solid rgb(204, 204, 204);">
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<p>
|
||
Incomplete genomes</p>
|
||
</td>
|
||
<td style="padding: 2px; width: 52%; border-bottom: 1px solid rgb(204, 204, 204);">
|
||
<p>
|
||
These can be whole genome shotgun (WGS) sequences. WGS submissions should be prepared using the <a href="https://www.ncbi.nlm.nih.gov/genbank/tbl2asn2.html">tbl2asn</a> or <a href="https://www.ncbi.nlm.nih.gov/Sequin/index.html">Sequin</a> tools. For assistance contact <a href="mailto:genomes@ncbi.nlm.nih.gov">genomes@ncbi.nlm.nih.gov</a> .</p>
|
||
</td>
|
||
<td style="padding: 2px; width: 24%; border-bottom: 1px solid rgb(204, 204, 204);">
|
||
<p align="center"><a href="https://www.ncbi.nlm.nih.gov/projects/genome/assembly/submission/index.shtml">Assembly submission information</a><br />
|
||
& <a href="https://www.ncbi.nlm.nih.gov/projects/genome/assembly/submission/index.shtml#ex">Examples</a></p>
|
||
<p align="center">
|
||
<a href="https://www.ncbi.nlm.nih.gov/genbank/wgs.html">WGS submissions</a>
|
||
</p>
|
||
</td>
|
||
</tr>
|
||
<tr>
|
||
<td style="padding: 2px; width: 24%; border-bottom: 1px solid rgb(204, 204, 204);">
|
||
<p>
|
||
High Throughput Genome Sequences (HTGSs)</p>
|
||
</td>
|
||
<td style="padding: 2px; width: 52%; border-bottom: 1px solid rgb(204, 204, 204);">
|
||
<p>
|
||
The clones (e.g. BACs) of large-scale clone-based genome sequencing projects that are to be released quickly into GenBank can be submitted via the HTGS system. Sequences that are to be kept confidential or are few in number should be submitted as described above for <em>Single nucleotide sequences</em>.</p>
|
||
<p>
|
||
HTGS submissions require prior communication with NCBI staff, so please read about the <a href="https://www.ncbi.nlm.nih.gov/HTGS/subinfo.html">HTGS submission process</a> for details.</p>
|
||
</td>
|
||
<td style="padding: 2px; width: 24%; border-bottom: 1px solid rgb(204, 204, 204);">
|
||
<p align="center">
|
||
<a href="https://www.ncbi.nlm.nih.gov/HTGS/subinfo.html">HTGS submissions</a>
|
||
</p>
|
||
</td>
|
||
</tr>
|
||
<tr style="border-bottom: 1px solid rgb(229, 229, 229);">
|
||
<td style="padding: 2px; width: 24%; background-color: rgb(255, 255, 255);">
|
||
</td>
|
||
<td style="padding: 2px; width: 52%; text-align: center; background-color: rgb(255, 255, 255);">
|
||
<p align="center">
|
||
<strong>Other Submission Types</strong>
|
||
</p>
|
||
</td>
|
||
<td style="padding: 2px; width: 22%; background-color: rgb(255, 255, 255);">
|
||
</td>
|
||
</tr>
|
||
<tr>
|
||
<td style="padding: 2px; width: 24%; border-bottom: 1px solid rgb(204, 204, 204);">
|
||
<p>
|
||
Barcode of Life sequences</p>
|
||
</td>
|
||
<td style="padding: 2px; width: 52%; border-bottom: 1px solid rgb(204, 204, 204);">
|
||
<p>
|
||
Mitochondrial cytochrome oxidase I sequences that are part of the Barcode of Life initiative can be submitted using a <a href="https://www.ncbi.nlm.nih.gov/WebSub/?tool=barcode">customized Bankit</a>.</p>
|
||
</td>
|
||
<td style="padding: 2px; width: 24%; border-bottom: 1px solid rgb(204, 204, 204);">
|
||
<p align="center">
|
||
<a href="https://www.ncbi.nlm.nih.gov/WebSub/?tool=barcode">Barcode submit page</a>
|
||
</p>
|
||
</td>
|
||
</tr>
|
||
<tr>
|
||
<td style="padding: 2px; width: 24%; border-bottom: 1px solid rgb(204, 204, 204);">
|
||
<p>
|
||
New sequence annotation for a <em>non-RefSeq</em> record submitted to GenBank by someone else</p>
|
||
</td>
|
||
<td style="padding: 2px; width: 52%; border-bottom: 1px solid rgb(204, 204, 204);">
|
||
<p>
|
||
Third Party Annotation (TPA) submissions can be created for annotation of existing GenBank records when the submitter has <em>experimental or inferential evidence</em> that will be published in a peer-reviewed biological journal.</p>
|
||
<p>
|
||
Please read about the TPA database and its submissions policies before submission.</p>
|
||
</td>
|
||
<td style="padding: 2px; width: 24%; border-bottom: 1px solid rgb(204, 204, 204);">
|
||
<p align="center">
|
||
<a href="https://www.ncbi.nlm.nih.gov/Genbank/TPA.html">TPA information</a>
|
||
</p>
|
||
<p align="center">
|
||
<a href="https://www.ncbi.nlm.nih.gov/genbank/tpafaq.html">TPA FAQs</a>
|
||
</p>
|
||
</td>
|
||
</tr>
|
||
<tr>
|
||
<td style="padding: 2px; width: 24%; border-bottom: 1px solid rgb(204, 204, 204);">
|
||
<p>
|
||
Computationally assembled transcript sequences</p>
|
||
</td>
|
||
<td style="padding: 2px; width: 52%; border-bottom: 1px solid rgb(204, 204, 204);">
|
||
<p>
|
||
These records, based on those that have already been submitted to SRA or the Trace Archive, may be candidates for submission to the Transcriptome Shotgun Assembly (TSA) repository.</p>
|
||
</td>
|
||
<td style="padding: 2px; width: 24%; border-bottom: 1px solid rgb(204, 204, 204);">
|
||
<p align="center">
|
||
<a href="https://www.ncbi.nlm.nih.gov/Genbank/TSA.html">TSA information</a>
|
||
</p>
|
||
</td>
|
||
</tr>
|
||
<tr>
|
||
<td style="padding: 2px; width: 24%; border-bottom: 1px solid rgb(204, 204, 204);">
|
||
<p>
|
||
Variations or Polymorphisms<sup>1</sup></p>
|
||
</td>
|
||
<td style="padding: 2px; width: 52%; border-bottom: 1px solid rgb(204, 204, 204);">
|
||
<p>
|
||
Single nucleotide polymorphisms as well as short insertions and deletions (<50bp) should be submitted to dbSNP, while large structural variations and copy number variation (CNV) data should be submitted to dbVar.</p>
|
||
<p>
|
||
Please note that human variations/polymorphisms with <em>clinical relevance</em> should be submitted to a specialized Human Variation Batch submission process using <a href="http://www.hgvs.org/mutnomen/">HGVS nomenclature</a>.</p>
|
||
</td>
|
||
<td style="padding: 2px; width: 24%; border-bottom: 1px solid rgb(204, 204, 204);">
|
||
<p align="center">
|
||
<a href="https://submit.ncbi.nlm.nih.gov/subs/variation/">Variation Submission Portal</a>
|
||
</p>
|
||
</td>
|
||
</tr>
|
||
<tr>
|
||
<td style="padding: 2px; width: 24%; border-bottom: 1px solid rgb(204, 204, 204);">
|
||
<p>
|
||
Primers, siRNAs, or probes</p>
|
||
</td>
|
||
<td style="padding: 2px; width: 52%; border-bottom: 1px solid rgb(204, 204, 204);">
|
||
<p>
|
||
Primer or nucleotide-based probe sequences should be submitted to the Probe Database.</p>
|
||
</td>
|
||
<td style="padding: 2px; width: 24%; border-bottom: 1px solid rgb(204, 204, 204);">
|
||
<p align="center">
|
||
<a href="https://www.ncbi.nlm.nih.gov/genome/probe/doc/Submitting.shtml">Probe submit page</a>
|
||
</p>
|
||
</td>
|
||
</tr>
|
||
<tr>
|
||
<td style="padding: 2px; width: 24%; border-bottom: 1px solid rgb(204, 204, 204);">
|
||
<p>
|
||
High throughput sequences</p>
|
||
</td>
|
||
<td style="padding: 2px; width: 52%; border-bottom: 1px solid rgb(204, 204, 204);">
|
||
<p>
|
||
The Sequence Read Archive (SRA) accepts reads from high throughput sequencing instruments. Some submissions include sets of SRA reads as part of a comprehensive package. <em>For the specific datasets described below,</em> please initiate submissions with the appropriate archive:</p>
|
||
<ul>
|
||
<li><em>Human sequence or metagenome sequence data </em>derived from clinical isolates or from sources with privacy concerns should be submitted to <a href="https://www.ncbi.nlm.nih.gov/gap/">dbGaP</a>.</li>
|
||
<li><em>Functional genomics studies </em>that examine gene expression, regulation or epigenomics (using methods such as RNA-Seq, miRNA-Seq, ChIP-Seq or methyl-Seq) should be submitted to <a href="https://www.ncbi.nlm.nih.gov/geo/info/seq.html">GEO</a>.</li>
|
||
<li><em>Transcript survey sequence assemblies </em>should go to the <a href="https://www.ncbi.nlm.nih.gov/Genbank/TSA.html">Transcriptome Shotgun Assembly (TSA)</a> archive.</li>
|
||
<li><em>Non-human and environmental metagenomics data </em>should go to the <a href="https://www.ncbi.nlm.nih.gov/genbank/metagenome.html">Metagenome</a> archive.</li>
|
||
<li><em>Whole genome sequence assemblies</em> should be submitted to <a href="https://www.ncbi.nlm.nih.gov/genbank/wgs.html">WGS</a>.</li>
|
||
<li><em>Capillary traces </em>should be deposited in the <a href="https://www.ncbi.nlm.nih.gov/genbank/wgs.html">Trace Archive</a>.</li>
|
||
<li><em>Sequences from the Barcode of Life project </em>should be submitted to <a href="https://www.ncbi.nlm.nih.gov/WebSub/?tool=barcode">Barcode</a>.</li>
|
||
</ul>
|
||
<p>
|
||
Curators of these resources will assist submitters in sending the data to SRA during the submission process.</p>
|
||
</td>
|
||
<td style="padding: 2px; width: 24%; border-bottom: 1px solid rgb(204, 204, 204);">
|
||
<p align="center">
|
||
For data types not mentioned to the left, submit directly to SRA:</p>
|
||
<p align="center">
|
||
<a href="https://trace.ncbi.nlm.nih.gov/Traces/sra_sub/sub.cgi?&m=submissions">SRA submit page</a>
|
||
<br />
|
||
<a href="https://www.ncbi.nlm.nih.gov/books/NBK47530/">SRA submission guidance</a>
|
||
</p>
|
||
</td>
|
||
</tr>
|
||
</tbody>
|
||
</table>
|
||
<p><sup>1</sup>If you need a GenBank accession number for Variation or Polymorphism submissions, you will need to annotate the variations as SNPs, insertions/deletions, or microsatellite regions on a nucleotide sequence and submit this to GenBank using the appropriate mechanism for the sequence type.</p>
|
||
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