Mercurial > repos > ktnyt > gembassy
diff GEMBASSY-1.0.3/doc/text/gcai.txt @ 2:8947fca5f715 draft default tip
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| author | ktnyt |
|---|---|
| date | Fri, 26 Jun 2015 05:21:44 -0400 |
| parents | 84a17b3fad1f |
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--- a/GEMBASSY-1.0.3/doc/text/gcai.txt Fri Jun 26 05:20:29 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,212 +0,0 @@ - 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. -