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gentrez |
gentrez searches NCBI Entrez with keyword through EUtilities.
This is intended for quick lookup through the command line
so only top ten hits are reported.
G-language SOAP service is provided by the
Institute for Advanced Biosciences, Keio University.
The original web service is located at the following URL:
http://www.g-language.org/wiki/soap
WSDL(RPC/Encoded) file is located at:
http://soap.g-language.org/g-language.wsdl
Documentation on G-language Genome Analysis Environment methods are
provided at the Document Center
http://ws.g-language.org/gdoc/
% gentrez genome 'Escherichia coli' Search NCBI Entrez ASCII text output file [genome.Escherichia coli.gentrez]: |
Qualifier | Type | Description | Allowed values | Default |
---|---|---|---|---|
Standard (Mandatory) qualifiers | ||||
[-database] (Parameter 1) |
string | NCBI database to search | Any string | pubmed |
[-query] (Parameter 2) |
string | Query to search | Any string | |
[-outfile] (Parameter 3) |
outfile | ASCII text output file | Output file | $(database).$(query).gentrez |
Additional (Optional) qualifiers | ||||
(none) | ||||
Advanced (Unprompted) qualifiers | ||||
(none) |
The database definitions for following commands are available at
http://soap.g-language.org/kbws/embossrc
gentrez reads no file input.
The output from gentrez is to a plain text file.
File: genome.Escherichia coli.gentrez
53 entries found in NUCLEOTIDE: (Showing up to 10 hits) 1. Accession Number: NZ_AKBV01000001 Escherichia coli str. K-12 substr. MG1655 strain K-12 cont1.1 chromosome, whole genome shotgun sequence, complete genome 2. Accession Number: NC_018658 Escherichia coli O104:H4 str. 2011C-3493 chromosome, complete genome 3. Accession Number: NC_012971 Escherichia coli BL21(DE3) chromosome, complete genome 4. Accession Number: NC_017635 Escherichia coli W chromosome, complete genome 5. Accession Number: NC_018650 Escherichia coli O104:H4 str. 2009EL-2050 chromosome, complete genome 6. Accession Number: NC_018661 Escherichia coli O104:H4 str. 2009EL-2071 chromosome, complete genome 7. Accession Number: NC_017906 Escherichia coli Xuzhou21 chromosome, complete genome 8. Accession Number: NC_017634 Escherichia coli O83:H1 str. NRG 857C chromosome, complete genome 9. Accession Number: NC_017656 Escherichia coli O55:H7 str. RM12579 chromosome, complete genome 10. Accession Number: NC_017664 Escherichia coli W chromosome, complete genome |
None.
None.
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.
None.
None.
It always exits with a status of 0.
None.
Program name | Description |
---|
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