Mercurial > repos > ktnyt > gembassy
view GEMBASSY-1.0.3/doc/text/gwvalue.txt @ 0:8300eb051bea draft
Initial upload
| author | ktnyt |
|---|---|
| date | Fri, 26 Jun 2015 05:19:29 -0400 |
| parents | |
| children |
line wrap: on
line source
gwvalue Function Calculate the 'relative adaptiveness of each codon' (W) Description gwvalue calculates the 'relative adaptiveness of each codon' (W value) which is essential in CAI analysis. W value is calculated by setting the best codon to 1 and calculating the proportion of the other codons. 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 gwvalue % gwvalue refseqn:NC_000913 Calculate the 'relative adaptiveness of each codon' (W) Codon usage output file [nc_000913.gwvalue]: 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 [*.gwvalue] Codon usage output file Additional (Optional) qualifiers: (none) Advanced (Unprompted) qualifiers: -include string [ribosomal.*protein] Regular expression to include genes in a reference set a reference set in several studies are in-built 1: Nakamura and Tabata, 2: Sharp and Li, 3: Sakai et al. (Any string) -exclude string [[Mm]itochondrial] Regular expression to exclude genes from a reference set (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 gwvalue reads one or more nucleotide sequences. Output file format The output from gwvalue is to a plain text file. File: nc_000913.gwvalue Sequence: NC_000913 Reference set of highly expressed genes product 30S ribosomal subunit protein S20 30S ribosomal subunit protein S2 ribosomal protein S12 methylthiotransferase; radical SAM superfamily ribosomal protein S6 modification protein 30S ribosomal subunit protein S1 ribosomal-protein-S5-alanine N-acetyltransferase 50S ribosomal subunit protein L32 [Part of this file has been deleted for brevity] T,acc,1.0000 T,acg,0.2234 T,act,0.9734 V,gta,0.4960 V,gtc,0.2281 V,gtg,0.3422 V,gtt,1.0000 W,tgg,1.0000 Y,tac,1.0000 Y,tat,0.5310 Data files None. Notes None. References Sharp PM et al. (2005) Variation in the strength of selected codon usage bias among bacteria, Nucleic Acids Res. 33(4):1141-1153 Sakai et al. (2001) Correlation between Shine--Dalgarno sequence conservation and codon usage of bacterial genes, J.Mol.Evol. 52:164-170. Nakamura and Tabata (1997) Codon-anticodon assignment and detection of codon usage trends in seven microbial genomes, Microb.Comp.Genomics 2:299-312. Sharp and Li (1987) The codon Adaptation Index--a measure of directional synonymous codon usage bias, and its potential applications, Nucleic Acids Res. 15:1281-1295. 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 genc Calculate the effective number of codons (Nc) gew Calculate a measure of synonymous codon usage evenness (Ew) gfop Calculate the frequency of optimal codons (Fop) gscs Calculates the scaled chi-square 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.