gdistincc

 

Function

Calculates the distance between two loci in circular chromosomes

Description

gdistincc calculates the distance between two loci in circular
chromosomes. It is mostly useful to calculate the distance from the
replication origin.

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 gdistincc

% gdistincc refseqn:NC_000913 1234
Calculates the distance between two loci in circular chromosomes
Output file [nc_000913.gdistincc]: 

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
[-first]
(Parameter 2)
integer Position to find the distance Any integer value 0
[-outfile]
(Parameter 3)
outfile Output file name Output file <*>.gdistincc
Additional (Optional) qualifiers
(none)
Advanced (Unprompted) qualifiers
-second integer If the second position is negative, position of replication origin is used Any integer value -1
-[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

gdistincc reads one or more nucleotide sequences.

Output file format

The output from gdistincc is to a plain text file.

File: nc_000913.gdistincc

Sequence: NC_000913 Position1: 1234 Distance 1169193600

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
gconsensusz Calculate consensus in given array of sequences
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.