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ggcsi |
ggcsi calculates the GC Skew Index (GCSI) of the given circular bacterial
genome. GCSI quantifies the degree of GC Skew. In other words, this index
represents the degree of strand-specific mutational bias in bacterial
genomes, caused by replicational selection.
GCSI is calculated by the following formula:
GCSI = sqrt((SA/6000) * (dist/600))
where SA is the spectral amplitude of Fourier power spectrum at 1Hz,
and dist is the normalized Euclidean distance between the vertices of
cumulative GC skew.
GCSI ranges from 0 (no observable skew) to 1 (strong skew), and Archaeal
genomes that have multiple replication origins and therefore have no
observable skew mostly have GCSI below 0.05. Escherichia coli genome has
values around 0.10.
Version 1 of GCSI required fixed number of windows (4096), but the new GCSI
version 2 (also known as generalized GCSI: gGCSI) is invariant of the number
of windows. GCSI version 1 is calculated as an arithmetic mean (as opposed
to the geometric mean of gGCSI) of SR (spectral ratio, the signal-to-noise
ratio of 1Hz power spectrum) and dist.
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/
% ggcsi refseqn:NC_000913 GC Skew Index: an index for strand-specific mutational bias Program compseq output file [nc_000913.ggcsi]: |
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 | Program compseq output file | Output file | <*>.ggcsi |
Additional (Optional) qualifiers | ||||
(none) | ||||
Advanced (Unprompted) qualifiers | ||||
-gcsi | selection | GCSI version to use | Choose from selection list of values | 2 |
-window | integer | Number of windows. Must be a power of 2 | 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 |
-at | boolean | Use AT skew for calculation | Boolean value Yes/No | No |
-pval | boolean | Calculate p-value when GCSI version 2 is selected | 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
ggcsi reads one or more nucleotide sequences.
The output from ggcsi is to a plain text file.
File: nc_000913.ggcsi
Sequence: NC_000913 GCSI: 0.0966615833014818 SA: 487.218569030757 DIST: 69.037726 |
None.
None.
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 |
---|---|
gb1 | Calculate strand bias of bacterial genome using B1 index |
gb2 | Calculate strand bias of bacterial genome using B2 index |
gdeltagcskew | Calculate strand bias of bacterial genome using delta GC skew |
gldabias | Calculate strand bias of bacterial genome using linear discriminant analysis (LDA) |
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