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gfindoriter |
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/
% gfindoriter refseqn:NC_000913 Predict the replication origin and terminus in bacterial genomes Output file [nc_000913.gfindoriter]: |
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 |
The database definitions for following commands are available at
http://soap.g-language.org/kbws/embossrc
gfindoriter reads one or more nucleotide sequences.
The output from gfindoriter is to a plain text file.
File: nc_000913.gfindoriter
?
Sequence: NC_000913 Origin: 3922946 Terminus: 1550274 |
None.
None.
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.
None.
None.
It always exits with a status of 0.
None.
Program name | Description |
---|---|
greporiter | Gets the positions of replication origin and terminus |
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