gconsensusz

 

Function

Calculate consensus in given array of sequences

Description

gconsensusz calculates the consensus of given list of sequences, using
Z-score. The Z-score will show higher values when the sequences are biased
to a single character within the list.

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 gconsensusz

% gconsensusz consensus.fasta
Calculate consensus in given array of sequences
Program compseq output file (optional) [rs_000000.gconsensusz]: 

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

Example 2

% gconsensusz consensus.fasta -plot -graph png
Calculate consensus in given array of sequences
Created gconsensusz.1.png

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
-graph xygraph Graph type EMBOSS has a list of known devices, including ps, hpgl, hp7470, hp7580, meta, cps, x11, tek, tekt, none, data, xterm, png, gif, svg EMBOSS_GRAPHICS value, or x11
-outfile outfile Program compseq output file (optional) Output file <*>.gconsensusz
Additional (Optional) qualifiers
(none)
Advanced (Unprompted) qualifiers
-high integer Z value greater than which is significant Any integer value 1
-low float Z value less than which is insignificant Any numeric value 0.2
-plot toggle Include to plot result Toggle value Yes/No No

Input file format

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

gconsensusz reads one or more nucleotide sequences.

Output file format

The output from gconsensusz is to a plain text file or the EMBOSS graphics device.

File: rs_000000.gconsensusz

0.487923290212298,1.74762197406504,0.487923290212298,1.74762197406504,4.26701934177052,1.74762197406504,0.487923290212298,3.00732065791778,0.487923290212298,0.487923290212298,0.487923290212298,0.487923290212298,3.00732065791778,0.487923290212298,1.74762197406504,1.74762197406504,0.487923290212298,1.74762197406504,1.74762197406504,1.74762197406504,1.74762197406504,0.487923290212298,0.487923290212298,0.487923290212298,0.487923290212298,3.00732065791778,1.74762197406504,1.74762197406504,1.74762197406504,0.487923290212298,1.74762197406504,1.74762197406504,1.74762197406504,1.74762197406504,0.487923290212298,1.74762197406504,1.74762197406504,0.487923290212298,1.74762197406504,0.487923290212298,1.74762197406504,1.74762197406504,1.74762197406504,0.487923290212298,0.487923290212298,1.74762197406504,1.74762197406504,3.00732065791778,1.74762197406504,0.487923290212298,1.74762197406504,1.74762197406504,1.74762197406504,1.74762197406504,1.74762197406504,0.487923290212298,0.487923290212298,1.74762197406504,1.74762197406504,0.487923290212298,0.487923290212298,0.487923290212298,1.74762197406504,1.74762197406504,1.74762197406504,1.74762197406504,3.00732065791778,0.487923290212298,3.00732065791778,1.74762197406504,3.00732065791778,0.487923290212298,1.74762197406504,1.74762197406504,3.00732065791778,1.74762197406504,0.487923290212298,1.74762197406504,1.74762197406504,1.74762197406504,0.487923290212298,1.74762197406504,1.74762197406504,0.487923290212298,1.74762197406504,0.487923290212298,0.487923290212298,1.74762197406504,1.74762197406504,0.487923290212298,0.487923290212298,3.00732065791778,5.52671802562326,3.00732065791778,3.00732065791778,1.74762197406504,1.74762197406504,1.74762197406504,1.74762197406504,0.487923290212298,0.487923290212298,0.487923290212298,1.74762197406504,0.487923290212298,0.487923290212298,0.487923290212298,3.00732065791778,1.74762197406504,0.487923290212298,0.487923290212298,1.74762197406504,0.487923290212298,1.74762197406504,1.74762197406504,1.74762197406504,0.487923290212298,1.74762197406504,1.74762197406504,0.487923290212298,1.74762197406504,0.487923290212298,1.74762197406504,0.487923290212298,0.487923290212298,3.00732065791778,1.74762197406504,0.487923290212298,1.74762197406504,1.74762197406504,3.00732065791778,1.74762197406504,1.74762197406504,0.487923290212298,0.487923290212298,1.74762197406504,1.74762197406504,0.487923290212298,1.74762197406504,1.74762197406504,1.74762197406504,1.74762197406504,3.00732065791778,1.74762197406504,1.74762197406504,0.487923290212298,1.74762197406504,0.487923290212298,0.487923290212298,0.487923290212298,0.487923290212298,1.74762197406504,0.487923290212298,1.74762197406504,1.74762197406504,0.487923290212298,1.74762197406504,1.74762197406504,1.74762197406504,0.487923290212298,0.487923290212298,0.487923290212298,1.74762197406504,0.487923290212298,0.487923290212298,1.74762197406504,1.74762197406504,0.487923290212298,0.487923290212298,1.74762197406504,3.00732065791778,1.74762197406504,1.74762197406504,0.487923290212298,1.74762197406504,1.74762197406504,1.74762197406504,0.487923290212298,0.487923290212298,1.74762197406504,1.74762197406504,0.487923290212298,1.74762197406504,0.487923290212298,1.74762197406504,1.74762197406504,1.74762197406504,0.487923290212298,3.00732065791778,1.74762197406504,1.74762197406504,1.74762197406504,0.487923290212298,1.74762197406504,1.74762197406504,1.74762197406504,0.487923290212298,0.487923290212298,1.74762197406504,1.74762197406504,0.487923290212298,1.74762197406504,1.74762197406504,0.487923290212298,1.74762197406504,0.487923290212298,3.00732065791778,1.74762197406504,3.00732065791778,1.74762197406504,0.487923290212298,3.00732065791778,3.00732065791778,3.00732065791778,0.487923290212298,0.487923290212298,1.74762197406504,0.487923290212298,0.487923290212298,1.74762197406504,0.487923290212298,0.487923290212298,0.487923290212298,1.74762197406504,0.487923290212298,1.74762197406504,0.487923290212298,1.74762197406504,1.74762197406504,0.487923290212298,0.487923290212298,3.00732065791778,1.74762197406504,0.487923290212298,0.487923290212298,0.487923290212298,1.74762197406504,1.74762197406504,1.74762197406504,1.74762197406504,1.74762197406504,1.74762197406504,1.74762197406504,0.487923290212298,1.74762197406504,1.74762197406504,1.74762197406504,4.26701934177052,0.487923290212298,3.00732065791778,0.487923290212298,1.74762197406504,1.74762197406504,0.487923290212298,1.74762197406504,1.74762197406504,1.74762197406504,1.74762197406504,1.74762197406504,3.00732065791778,3.00732065791778,4.26701934177052,1.74762197406504,1.74762197406504,0.487923290212298,0.487923290212298,1.74762197406504,0.487923290212298,0.487923290212298,0.487923290212298,1.74762197406504,0.487923290212298,0.487923290212298,3.00732065791778,1.74762197406504,3.00732065791778,1.74762197406504,1.74762197406504,1.74762197406504,1.74762197406504,1.74762197406504,0.487923290212298,0.487923290212298,3.00732065791778,3.00732065791778,1.74762197406504,1.74762197406504,1.74762197406504,3.0073206579177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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
gdistincc Calculates the distance between two loci in circular chromosomes
gpalindrome Searches palindrome sequences
gseqinfo Prints out basic nucleotide sequence statistics

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.