Difference between revisions of "GenBank"
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<font color="#800080" size="4"><strong>GenBank</strong></font><br /> | <font color="#800080" size="4"><strong>GenBank</strong></font><br /> | ||
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| − | <p>The <strong>GenBank</strong | + | <p>The <strong>GenBank</strong> sequence database is an open access, annotated collection of all publicly available nucleotide sequences and their protein translations. This database is produced at National Center for Biotechnology Information (NCBI) as part of the International Nucleotide Sequence Database Collaboration, or INSDC. GenBank and its collaborators receive sequences produced in laboratories throughout the world from more than 100,000 distinct organisms. GenBank continues to grow at an exponential rate, doubling every 10 months. Release 155, produced in August 2006, contained over 65 billion nucleotide bases in more than 61 million sequences. GenBank is built by direct submissions from individual laboratories, as well as from bulk submissions from large-scale sequencing centers.</p> |
| − | <p>Direct submissions are made to GenBank using | + | <p>Direct submissions are made to GenBank using BankIt, which is a Web-based form, or the stand-alone submission program, Sequin. Upon receipt of a sequence submission, the GenBank staff assigns an Accession number to the sequence and performs quality assurance checks. The submissions are then released to the public database, where the entries are retrievable by Entrez or downloadable by FTP. Bulk submissions of Expressed Sequence Tag (EST), Sequence Tagged Site (STS), Genome Survey Sequence (GSS), and High-Throughput Genome Sequence (HTGS) data are most often submitted by large-scale sequencing centers. The GenBank direct submissions group also processes complete microbial genome sequences.</p> |
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| − | <p> | ||
<h2><span class="editsection"></span><span class="mw-headline">History</span></h2> | <h2><span class="editsection"></span><span class="mw-headline">History</span></h2> | ||
| − | <p> | + | <p>Walter Goad of the Theoretical Biology and Biophysics Group at Los Alamos National Laboratory and others established the Los Alamos Sequence Database in 1979, which culminated in 1982 with the creation of the public GenBank funded by the National Institutes of Health, the National Science Foundation, the Department of Energy and the Department of Defense. LANL collaborated on GenBank with the firm Bolt, Beranek, and Newman, and by the end of 1983 more than 2,000 sequences were stored in it.</p> |
| − | <p>In the mid 1980s, the Intelligenetics bioinformatics company at | + | <p>In the mid 1980s, the Intelligenetics bioinformatics company at Stanford University managed the GenBank project in collaboration with LANL. As one of the earliest bioinformatics community projects on the Internet, the GenBank project started BIOSCI/Bionet news groups for promoting open access communications among bioscientists. During 1989 to 1992, the GenBank project transitioned to the newly created National Center for Biotechnology Information.</p> |
<p><a id="Growth_of_GenBank" name="Growth_of_GenBank"></a></p> | <p><a id="Growth_of_GenBank" name="Growth_of_GenBank"></a></p> | ||
<h2><span class="editsection"></span><span class="mw-headline">Growth of GenBank</span></h2> | <h2><span class="editsection"></span><span class="mw-headline">Growth of GenBank</span></h2> | ||
| − | <p>The | + | <p>The GenBank release notes for release 162.0 (October, 2007) state that "from 1982 to the present, the number of bases in GenBank has doubled approximately every 18 months." The following plot clearly shows the exponential growth. (On a semi-log scale such as this, a straight line represents an exponential change.)</p> |
| − | <p | + | <p><img height="395" alt="Growth in GenBank base pairs, 1982 to 2007" width="500" border="0" src="http://upload.wikimedia.org/wikipedia/commons/thumb/e/e4/Growth_of_Genbank.svg/500px-Growth_of_Genbank.svg.png" /></p> |
<p>The GenBank database includes additional data sets which are constructed mechanically from the main sequence data collection, and therefore are excluded from this count.</p> | <p>The GenBank database includes additional data sets which are constructed mechanically from the main sequence data collection, and therefore are excluded from this count.</p> | ||
<p><a id="See_also" name="See_also"></a></p> | <p><a id="See_also" name="See_also"></a></p> | ||
<h2><span class="editsection"></span><span class="mw-headline">See also</span></h2> | <h2><span class="editsection"></span><span class="mw-headline">See also</span></h2> | ||
<ul> | <ul> | ||
| − | <li | + | <li>Ensembl </li> |
| − | <li | + | <li>HPRD </li> |
| − | <li | + | <li>Sequence analysis </li> |
| − | <li | + | <li>Sequence profiling tool </li> |
| − | <li | + | <li>Sequence motif </li> |
| − | <li | + | <li>UniProt </li> |
| − | <li | + | <li>List of sequenced eukaryotic genomes </li> |
| − | <li> | + | <li>List of sequenced archeal genomes </li> |
</ul> | </ul> | ||
<p><a id="References" name="References"></a></p> | <p><a id="References" name="References"></a></p> | ||
<h2><span class="editsection"></span><span class="mw-headline">References</span></h2> | <h2><span class="editsection"></span><span class="mw-headline">References</span></h2> | ||
<ul> | <ul> | ||
| − | <li | + | <li>Walter Goad, GenBank founder, obituary </li> |
| − | <li><cite style="FONT-STYLE: normal">Benton, D. (1990). " | + | <li><cite style="FONT-STYLE: normal">Benton, D. (1990). "Recent changes in the GenBank On-line Service.". <em>Nucleic Acids Research</em> <strong>18</strong> (6): 1517–1520.</cite><span class="Z3988" title="ctx_ver=Z39.88-2004&rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&rft.genre=article&rft.atitle=Recent+changes+in+the+GenBank+On-line+Service.&rft.jtitle=Nucleic+Acids+Research&rft.date=1990&rft.volume=18&rft.issue=6&rft.au=Benton%2C+D.&rft.pages=1517%E2%80%931520&rft_id=http%3A%2F%2Fwww.pubmedcentral.gov%2Fpagerender.fcgi%3Fartid%3D330520"> </span> </li> |
| − | <li | + | <li>LANL GenBank History </li> |
| − | <li><cite style="FONT-STYLE: normal">Benton, D. <em>et al.</em> (2006). " | + | <li><cite style="FONT-STYLE: normal">Benton, D. <em>et al.</em> (2006). "GenBank". <em>Nucleic Acids Research</em> <strong>34</strong> (Database): D16-D20.</cite><span class="Z3988" title="ctx_ver=Z39.88-2004&rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&rft.genre=article&rft.atitle=GenBank&rft.jtitle=Nucleic+Acids+Research&rft.date=2006&rft.volume=34&rft.issue=Database&rft.au=Benton%2C+D.+%27%27et+al.%27%27&rft.pages=D16-D20&rft_id=http%3A%2F%2Fnar.oxfordjournals.org%2Fcgi%2Fcontent%2Fabstract%2F34%2Fsuppl_1%2FD16"> </span> </li> |
</ul> | </ul> | ||
<p><a id="External_links" name="External_links"></a></p> | <p><a id="External_links" name="External_links"></a></p> | ||
<h2><span class="editsection"></span><span class="mw-headline">External links</span></h2> | <h2><span class="editsection"></span><span class="mw-headline">External links</span></h2> | ||
<ul> | <ul> | ||
| − | <li | + | <li>GenBank </li> |
| − | <li | + | <li>Example sequence record, for hemoglobin beta </li> |
| − | <li | + | <li>BankIt </li> |
| − | <li> | + | <li>Sequin </li> |
| − | <li | + | <li>Emboss </li> |
</ul> | </ul> | ||
<p><a id="Sources" name="Sources"></a></p> | <p><a id="Sources" name="Sources"></a></p> | ||
<h2><span class="editsection"></span><span class="mw-headline">Sources</span></h2> | <h2><span class="editsection"></span><span class="mw-headline">Sources</span></h2> | ||
<ul> | <ul> | ||
| − | <li><em>This article contains material text from the</em | + | <li><em>This article contains material text from the</em> NCBI Handbook <em>published by the National Center for Biotechnology Information, which, as a US government publication, is in the public domain.</em> </li> |
</ul> | </ul> | ||
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Revision as of 21:14, 13 December 2007
GenBank
The GenBank sequence database is an open access, annotated collection of all publicly available nucleotide sequences and their protein translations. This database is produced at National Center for Biotechnology Information (NCBI) as part of the International Nucleotide Sequence Database Collaboration, or INSDC. GenBank and its collaborators receive sequences produced in laboratories throughout the world from more than 100,000 distinct organisms. GenBank continues to grow at an exponential rate, doubling every 10 months. Release 155, produced in August 2006, contained over 65 billion nucleotide bases in more than 61 million sequences. GenBank is built by direct submissions from individual laboratories, as well as from bulk submissions from large-scale sequencing centers.
Direct submissions are made to GenBank using BankIt, which is a Web-based form, or the stand-alone submission program, Sequin. Upon receipt of a sequence submission, the GenBank staff assigns an Accession number to the sequence and performs quality assurance checks. The submissions are then released to the public database, where the entries are retrievable by Entrez or downloadable by FTP. Bulk submissions of Expressed Sequence Tag (EST), Sequence Tagged Site (STS), Genome Survey Sequence (GSS), and High-Throughput Genome Sequence (HTGS) data are most often submitted by large-scale sequencing centers. The GenBank direct submissions group also processes complete microbial genome sequences.
History
Walter Goad of the Theoretical Biology and Biophysics Group at Los Alamos National Laboratory and others established the Los Alamos Sequence Database in 1979, which culminated in 1982 with the creation of the public GenBank funded by the National Institutes of Health, the National Science Foundation, the Department of Energy and the Department of Defense. LANL collaborated on GenBank with the firm Bolt, Beranek, and Newman, and by the end of 1983 more than 2,000 sequences were stored in it.
In the mid 1980s, the Intelligenetics bioinformatics company at Stanford University managed the GenBank project in collaboration with LANL. As one of the earliest bioinformatics community projects on the Internet, the GenBank project started BIOSCI/Bionet news groups for promoting open access communications among bioscientists. During 1989 to 1992, the GenBank project transitioned to the newly created National Center for Biotechnology Information.
Growth of GenBank
The GenBank release notes for release 162.0 (October, 2007) state that "from 1982 to the present, the number of bases in GenBank has doubled approximately every 18 months." The following plot clearly shows the exponential growth. (On a semi-log scale such as this, a straight line represents an exponential change.)
The GenBank database includes additional data sets which are constructed mechanically from the main sequence data collection, and therefore are excluded from this count.
See also
- Ensembl
- HPRD
- Sequence analysis
- Sequence profiling tool
- Sequence motif
- UniProt
- List of sequenced eukaryotic genomes
- List of sequenced archeal genomes
References
- Walter Goad, GenBank founder, obituary
- Benton, D. (1990). "Recent changes in the GenBank On-line Service.". Nucleic Acids Research 18 (6): 1517–1520.
- LANL GenBank History
- Benton, D. et al. (2006). "GenBank". Nucleic Acids Research 34 (Database): D16-D20.
External links
- GenBank
- Example sequence record, for hemoglobin beta
- BankIt
- Sequin
- Emboss
Sources
- This article contains material text from the NCBI Handbook published by the National Center for Biotechnology Information, which, as a US government publication, is in the public domain.
