gfindoriter

 

Function

Predict the replication origin and terminus in bacterial genomes

Description

gfindoriter predicts the replicational origin and terminus in circular
bacterial genomes, by taking the vertices of cumulative skew graphs (GC,
d keto, or purine). See Frank and Lobry (2000) for the basic idea behind
this algorithm (but also note that this algorithm is different from that
of Oriloc, which uses GC3 of genes).
Terminus of replication can be more accurate by using noise-reduction
filtering using Fourier spectrum of the GC skew. This low-pass filtering
can be applied using -filter option. See Arakawa et al. (2007) for details.

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 gfindoriter

% gfindoriter refseqn:NC_000913
Predict the replication origin and terminus in bacterial genomes
Output file [nc_000913.gfindoriter]: 

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 Output file name Output file <*>.gfindoriter
Additional (Optional) qualifiers
(none)
Advanced (Unprompted) qualifiers
-window integer Number of windows to use for Fat Fourier Transform. Only active when -lowpass option is specified. Value must be the power of two Any integer value 4096
-purine boolean Use purine skew for calculation Boolean value Yes/No No
-keto boolean Use keto skew for calculation Boolean value Yes/No No
-lowpass integer Lowpass filter strength in percent. Typically 95 or 99 works best Any integer value 0
-[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

gfindoriter reads one or more nucleotide sequences.

Output file format

The output from gfindoriter is to a plain text file.

File: nc_000913.gfindoriter

?
Sequence: NC_000913 Origin: 3922946 Terminus: 1550274

Data files

None.

Notes

None.

References

   Frank AC, Lobry JR (2000) Oriloc: prediction of replication boundaries in
      unannotated bacterial chromosomes, Bioinformatics, 16:566-567.

   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
greporiter Gets the positions of replication origin and terminus

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 scripts.

Comments

None.