gbasezvalue

 

Function

Extracts conserved oligomers per position using Z-score

Description

This function calculates and extracts conserved oligomers per position using
Z-score, in regions around the start/stop codons. The oligomers are returned
in ranking order up to "-limit" number.

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/

Usage

Here is a sample session with gbasezvalue

% gbasezvalue refseqn:NC_000913
Extracts conserved oligomers per position using Z-score
Program compseq output file (optional) [nc_000913.gbasezvalue]: 

Go to the input files for this example
Go to the output files for this example

Command line arguments

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 (optional) Output file <*>.gbasezvalue
Additional (Optional) qualifiers
(none)
Advanced (Unprompted) qualifiers
-limit integer Rank threshold for showing the conserved oligomer Any integer value 5
-position selection Either 'start' (around start codon) or 'end' (around stop codon) to create the PWM Choose from selection list of values start
-patlen integer Length of oligomer to count Any integer value 3
-upstream integer Length upstream of specified position to create PWM Any integer value 30
-downstream integer Length downstream of specified position to create PWM Any integer value 30
-[no]accid boolean Include to use sequence accession ID as query Boolean value Yes/No Yes

Input file format

The database definitions for following commands are available at
http://soap.g-language.org/kbws/embossrc

gbasezvalue reads one or more nucleotide sequences.

Output file format

The output from gbasezvalue is to a plain text file.

File: nc_000913.gbasezvalue

Sequence: NC_000913
position:-30,1,taa,-0.76525
2,aga,-0.79101
3,tta,-1.14174
4,cta,-1.18831
5,aat,-1.86652
position:-29,1,cta,-0.18368
2,aat,-0.71851
3,gac,-1.26182
4,taa,-1.39455

[Part of this file has been deleted for brevity]

position:29,1,gct,1.66288
2,act,1.26637
3,tat,0.66721
4,cct,-0.43158
5,tgt,-0.59254
position:30,1,ctg,3.12072
2,att,0.04193
3,ctc,-0.12416
4,cta,-0.38461
5,tta,-0.76413

Data files

None.

Notes

None.

References

   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.

Warnings

None.

Diagnostic Error Messages

None.

Exit status

It always exits with a status of 0.

Known bugs

None.

See also

Program name Description
gbase_counter Creates a position weight matrix of oligomers around start codon
gview_cds Displays a graph of nucleotide contents around start and stop codons

Author(s)

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

History

2012 - Written by Hidetoshi Itaya

Target users

This program is intended to be used by everyone and everything, from naive users to embedded scrips.

Comments

None.