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greporiter |
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/
% greporiter refseqn:NC_000913 Get the positions of replication origin and terminus Output file [nc_000913.greporiter]: |
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 |
The database definitions for following commands are available at
http://soap.g-language.org/kbws/embossrc
greporiter reads one or more nucleotide sequences.
The output from greporiter is to a plain text file.
File: nc_000913.greporiter
Sequence: NC_000913 Origin: 3923881 Terminus: 1550412 |
None.
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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.
None.
None.
It always exits with a status of 0.
None.
Program name | Description |
---|---|
gfindoriter | Predicts the replication origin and terminus in bacterial |
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