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<TITLE> EMBOSS: gentrez </TITLE>
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<A HREF="/" ONMOUSEOVER="self.status='Go to the EMBOSS home page';return true"><img border=0 src="http://soap.g-language.org/gembassy/emboss_explorer/manual/emboss_icon.jpg" alt="" width=150 height=48></a>
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gentrez
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<H2> Function </H2>
Search NCBI Entrez
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<H2>Description</H2>
<p>
gentrez searches NCBI Entrez with keyword through EUtilities. <br />
This is intended for quick lookup through the command line<br />
so only top ten hits are reported.<br />
<br />
G-language SOAP service is provided by the<br />
Institute for Advanced Biosciences, Keio University.<br />
The original web service is located at the following URL:<br />
<br />
http://www.g-language.org/wiki/soap<br />
<br />
WSDL(RPC/Encoded) file is located at:<br />
<br />
http://soap.g-language.org/g-language.wsdl<br />
<br />
Documentation on G-language Genome Analysis Environment methods are<br />
provided at the Document Center<br />
<br />
http://ws.g-language.org/gdoc/<br />
<br />
</p>
<H2>Usage</H2>
Here is a sample session with gentrez
<table width="90%"><tr><td bgcolor="#CCFFFF"><pre>
% gentrez genome 'Escherichia coli'
Search NCBI Entrez
ASCII text output file [genome.Escherichia coli.gentrez]:
</pre></td></tr></table>
Go to the <a href="#input">input files</a> for this example<br>
Go to the <a href="#output">output files</a> for this example<br><br>
<h2>Command line arguments</h2>
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<th align="left">Qualifier</th>
<th align="left">Type</th>
<th align="left">Description</th>
<th align="left">Allowed values</th>
<th align="left">Default</th>
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<th align="left" colspan=5>Standard (Mandatory) qualifiers</th>
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<td>[-database]<br>(Parameter 1)</td>
<td>string</td>
<td>NCBI database to search</td>
<td>Any string</td>
<td>pubmed</td>
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<td>[-query]<br>(Parameter 2)</td>
<td>string</td>
<td>Query to search</td>
<td>Any string</td>
<td> </td>
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<td>[-outfile]<br>(Parameter 3)</td>
<td>outfile</td>
<td>ASCII text output file</td>
<td>Output file</td>
<td>$(database).$(query).gentrez</td>
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<th align="left" colspan=5>Additional (Optional) qualifiers</th>
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<td colspan=5>(none)</td>
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<th align="left" colspan=5>Advanced (Unprompted) qualifiers</th>
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<td colspan=5>(none)</td>
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<h2 id="input">Input file format</h2>
<p>
The database definitions for following commands are available at<br />
http://soap.g-language.org/kbws/embossrc<br />
<br />
gentrez reads no file input.<br />
<br />
</p>
<h2 id="output">Output file format</h2>
<p>
The output from gentrez is to a plain text file.<br />
<br />
File: genome.Escherichia coli.gentrez<br />
<br />
<table width="90%"><tr><td bgcolor="#CCFFCC">
53 entries found in NUCLEOTIDE: (Showing up to 10 hits)<br />
<br />
1. Accession Number: NZ_AKBV01000001<br />
Escherichia coli str. K-12 substr. MG1655 strain K-12 cont1.1 chromosome, whole genome shotgun sequence, complete genome<br />
<br />
2. Accession Number: NC_018658<br />
Escherichia coli O104:H4 str. 2011C-3493 chromosome, complete genome<br />
<br />
3. Accession Number: NC_012971<br />
Escherichia coli BL21(DE3) chromosome, complete genome<br />
<br />
4. Accession Number: NC_017635<br />
Escherichia coli W chromosome, complete genome<br />
<br />
5. Accession Number: NC_018650<br />
Escherichia coli O104:H4 str. 2009EL-2050 chromosome, complete genome<br />
<br />
6. Accession Number: NC_018661<br />
Escherichia coli O104:H4 str. 2009EL-2071 chromosome, complete genome<br />
<br />
7. Accession Number: NC_017906<br />
Escherichia coli Xuzhou21 chromosome, complete genome<br />
<br />
8. Accession Number: NC_017634<br />
Escherichia coli O83:H1 str. NRG 857C chromosome, complete genome<br />
<br />
9. Accession Number: NC_017656<br />
Escherichia coli O55:H7 str. RM12579 chromosome, complete genome<br />
<br />
10. Accession Number: NC_017664<br />
Escherichia coli W chromosome, complete genome<br />
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<h2>Data files</h2>
<p>
None.
</p>
<h2>Notes</h2>
<p>
None.
</p>
<h2>References</h2>
<pre>
Arakawa, K., Mori, K., Ikeda, K., Matsuzaki, T., Konayashi, Y., and
Tomita, M. (2003) G-language Genome Analysis Environment: A Workbench
for Nucleotide Sequence Data Mining, Bioinformatics, 19, 305-306.
Arakawa, K. and Tomita, M. (2006) G-language System as a Platform for
large-scale analysis of high-throughput omics data, J. Pest Sci.,
31, 7.
Arakawa, K., Kido, N., Oshita, K., Tomita, M. (2010) G-language Genome
Analysis Environment with REST and SOAP Web Service Interfaces,
Nucleic Acids Res., 38, W700-W705.
</pre>
<h2>Warnings</h2>
<p>
None.
</p>
<h2>Diagnostic Error Messages</h2>
<p>
None.
</p>
<h2>Exit status</h2>
<p>
It always exits with a status of 0.
</p>
<h2>Known bugs</h2>
<p>
None.
</p>
<h2>See also</h2>
<table border cellpadding=4 bgcolor="#FFFFF0"><tr><th>Program name</th>
<th>Description</th></tr>
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<h2>Author(s)</h2>
<pre>
Hidetoshi Itaya (celery@g-language.org)
Institute for Advanced Biosciences, Keio University
252-0882 Japan
Kazuharu Arakawa (gaou@sfc.keio.ac.jp)
Institute for Advanced Biosciences, Keio University
252-0882 Japan</pre>
<h2>History</h2>
2012 - Written by Hidetoshi Itaya
<h2>Target users</h2>
This program is intended to be used by everyone and everything, from
naive users to embedded scrips.
<h2>Comments</h2>
None.
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