|   | gpalindrome | 
   gpalindrome searches for palindrome sequences in the genome.
   Search parameters can be changed for more efficient searches, and g-t
   matching can be specified by passing the "-gtmatch" qualifier.
    
   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/
| % gpalindrome refseqn:NC_000913 Searches palindrome sequences Program compseq output file [nc_000913.gpalindrome]: | 
| Qualifier | Type | Description | Allowed values | Default | 
|---|---|---|---|---|
| Standard (Mandatory) qualifiers | ||||
| [-sequence] (Parameter 1) | seqall | Nucleotide sequence(s) filename and optional format, or reference (input USA) | Readable sequence(s) | Required | 
| [-outfile] (Parameter 2) | outfile | Program compseq output file | Output file | <*>.gpalindrome | 
| Additional (Optional) qualifiers | ||||
| (none) | ||||
| Advanced (Unprompted) qualifiers | ||||
| -shortest | integer | Shortest palindrome to search | Any integer value | 4 | 
| -loop | integer | Longest stem loop to allow | Any integer value | 0 | 
| -gtmatch | boolean | If 1, allows g-t match | Boolean value Yes/No | No | 
| -[no]accid | boolean | Include to use sequence accession ID as query | Boolean value Yes/No | Yes | 
   The database definitions for following commands are available at
   http://soap.g-language.org/kbws/embossrc
   gpalindrome reads one or more nucleotide sequences.
   The output from gpalindrome is to a plain text file.
   File: nc_000913.gpalindrome
| Sequence: NC_000913 Length, start, end, sequence 4,16,18,tg ca 4,27,29,at at 4,44,46,tt aa 4,67,69,ag ct 4,97,99,aa tt 4,99,101,tt aa 10,100,108,taaaa tttta 4,132,134,tt aa [Part of this file has been deleted for brevity] 4,4639484,4639486,tg ca 6,4639487,4639491,aag ctt 4,4639495,4639497,cg cg 4,4639506,4639508,ca tg 6,4639552,4639556,gtc gac 4,4639607,4639609,tg ca 4,4639619,4639621,tg ca 4,4639621,4639623,ca tg 4,4639625,4639627,at at 4,4639637,4639639,at at | 
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 | 
|---|---|
| gconsensusz | Calculate consensus in given array of sequences | 
| gdistincc | Calculates the distance between two loci in circular chromosomes | 
| gseqinfo | Prints out basic nucleotide sequence statistics | 
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