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gkmertable |
gkmertable creates an image showing the abundance of all k-mers
(oligonucleotides of length k) in a given sequence. For example, for
tetramers (k=4), resulting image is composed of 4^4 = 256 boxes, each
representing an oligomer. Oligomer name and abundance is written within
these boxes, and abundance is also visualized with the box color, from
white (none) to black (highly frequent).
This k-mer table is alternatively known as the FCGR (frequency matrices
extracted from Chaos Game Representation).
Position of the oligomers can be recursively located as follows:
For each letter in an oligomer, a box is subdivided into four quadrants,
where A is upper left, T is lower right, G is upper right, and C is lower
left.
Therefore, oligomer ATGC is in the
A = upper left quadrant
T = lower right within the above quadrant
G = upper right within the above quadrant
C = lower left within the above quadrant
More detailed documentation is available at
http://www.g-language.org/wiki/cgr
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/
Here is a sample session with gkmertable % gkmertable refseqn:NC_000913 Create an image showing all k-mer abundance within a sequence Created gkmertable.1.png Go to the input files for this example Go to the output files for this example |
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 |
Additional (Optional) qualifiers | ||||
(none) | ||||
Advanced (Unprompted) qualifiers | ||||
-format | string | Output file format. Dependent on 'convert' command | Any string | png |
-k | integer | Length of oligomer | Any integer value | 6 |
-goutfile | string | Output file for non interactive displays | Any string | gkmertable |
The database definitions for following commands are available at
http://soap.g-language.org/kbws/embossrc
gkmertable reads one or more nucleotide sequences.
The output from gkmertable is to an image file.
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 |
---|---|
gnucleotideperiodicity | Checks the periodicity of certain oligonucleotides |
goligomercounter | Counts the number of given oligomers in a sequence |
goligomersearch | Searches oligomers in given sequence |
gsignature | Calculate oligonucleotide usage (genomic signature) |
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