greporiter

 

Function

Get the positions of replication origin and terminus

Description

greporiter returns the positions of replication origin and terminus
in bacterial genomes by several means.

1. Use of databases
By default, grep_ori_ter tries to retrieve the position of replication
origin in DoriC Gao and Zhang (2007) database, and the position of
replication terminus from the supplemental data provided in
Kono et al. (2011).
If the position of origin cannot be found in the database, but "rep_origin"
feature is available, center position within this feature is used for
origin.

2. Oriloc
Using -orilocoption, you can predict the replication origin and
terminus using the popular Oriloc program developed by Lobry et al.
available as part of the SeqinR package Frank and Lobry (2000).

3. Use GC skew shift-point
If the positions of origin or terminus cannot be found in the databases,
grep_ori_ter automatically calls find_ori_ter() method to predict the
positions using GC skew shift-points at one-base-pair resolution.

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 greporiter

% greporiter refseqn:NC_000913
Get the positions of replication origin and terminus
Output file [nc_000913.greporiter]: 

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 <*>.greporiter
Additional (Optional) qualifiers
(none)
Advanced (Unprompted) qualifiers
-oriloc boolean Include Oriloc for prediction Boolean value Yes/No No
-gcskew boolean Include to use GC skew shift-point for prediction Boolean value Yes/No No
-difthreshold integer Distance between the GC skew shift point and predicted dif site expressed as the precentage of genome size, used as a threshold to retrieve dif sequence from the database Any integer value 0
-dbonly boolean Include to only use values available in databases and to suppress prediction Boolean value Yes/No No
-[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

greporiter reads one or more nucleotide sequences.

Output file format

The output from greporiter is to a plain text file.

File: nc_000913.greporiter

Sequence: NC_000913 Origin: 3923881 Terminus: 1550412

Data files

None.

Notes

None.

References

   Gao F and Zhang CT (2007) DoriC: a database of oriC regions in bacterial
      genomes, Bioinformatics, 23(14):1866-1867

   Kono N et al. (2011) Comprehensive prediction of chromosome dimer resolution 
      sites in bacterial genomes, BMC Genomics, 12(1):19

   Frank AC and Lobry JR (2000) "Oriloc: prediction of replication boundaries 
      in unannotated bacterial chromosomes", Bioinformatics, 16(6):560-561

   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
gfindoriter Predicts the replication origin and terminus in bacterial

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.