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| date | Fri, 26 Jun 2015 05:20:29 -0400 |
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gcai Function Calculate codon adaptation index for each gene Description gcai calculates codon adaptation index (CAI) for each gene. CAI is measure a of the relative adaptiveness of the codon usage of a gene towards the codon usage of highly expressed genes, ranging from 0 (no bias) to 1 (maximum bias). CAI can be used as a 'universal' measure of codon usage bias as it is correlated with various gene features such as gene expression level, GC content, and GC skew. The CAI for a gene where A(i) is the amino acid at position i and W(A) is the W value corresponding to the amino acid is calculated as follows: CAI = sum(log(e,W(A(i)))) 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 gcai % gcai refseqn:NC_000913 Calculate codon adaptation index for each gene Codon usage output file [nc_000913.gcai]: Go to the input files for this example Go to the output files for this example Command line arguments Standard (Mandatory) qualifiers: [-sequence] seqall Nucleotide sequence(s) filename and optional format, or reference (input USA) [-outfile] outfile [*.gcai] Codon usage output file Additional (Optional) qualifiers: (none) Advanced (Unprompted) qualifiers: -translate boolean [N] Include when translating using standard codon table -wabsent string [-1] W value of codons absent from a reference set to negative when excludes such codons from the calculation (Any string) -[no]accid boolean [Y] Include to use sequence accession ID as query Associated qualifiers: "-sequence" associated qualifiers -sbegin1 integer Start of each sequence to be used -send1 integer End of each sequence to be used -sreverse1 boolean Reverse (if DNA) -sask1 boolean Ask for begin/end/reverse -snucleotide1 boolean Sequence is nucleotide -sprotein1 boolean Sequence is protein -slower1 boolean Make lower case -supper1 boolean Make upper case -scircular1 boolean Sequence is circular -sformat1 string Input sequence format -iquery1 string Input query fields or ID list -ioffset1 integer Input start position offset -sdbname1 string Database name -sid1 string Entryname -ufo1 string UFO features -fformat1 string Features format -fopenfile1 string Features file name "-outfile" associated qualifiers -odirectory2 string Output directory General qualifiers: -auto boolean Turn off prompts -stdout boolean Write first file to standard output -filter boolean Read first file from standard input, write first file to standard output -options boolean Prompt for standard and additional values -debug boolean Write debug output to program.dbg -verbose boolean Report some/full command line options -help boolean Report command line options and exit. More information on associated and general qualifiers can be found with -help -verbose -warning boolean Report warnings -error boolean Report errors -fatal boolean Report fatal errors -die boolean Report dying program messages -version boolean Report version number and exit Input file format The database definitions for following commands are available at http://soap.g-language.org/kbws/embossrc gcai reads one or more nucleotide sequences. Output file format The output from gcai is to a plain text file. File: nc_000913.gcai Sequence: NC_000913 cai,gene 0.7256,thrL 0.4831,thrA 0.4719,thrB 0.5178,thrC 0.4989,yaaX 0.4933,yaaA 0.4533,yaaJ 0.7074,talB [Part of this file has been deleted for brevity] 0.4681,yjjX 0.4797,ytjC 0.5350,rob 0.4932,creA 0.3918,creB 0.4170,creC 0.4167,creD 0.6466,arcA 0.4236,yjjY 0.3913,yjtD Data files None. Notes None. References Sharp PM, Li WH. (1987) The codon Adaptation Index--a measure of directional synonymous codon usage bias, and its potential applications. Nucleic Acids Res. 15(3):1281-95. 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 gp2 Calculate the P2 index of each gene gphx Identify predicted highly expressed gene 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 2013 - Fixed by Hidetoshi Itaya Target users This program is intended to be used by everyone and everything, from naive users to embedded scripts. Comments None.