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| author | ktnyt |
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| date | Fri, 26 Jun 2015 05:19:29 -0400 |
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gfop Function Calculate the frequency of optimal codons (Fop) Description gfop calculates the frequency of optimal codons (Fop).Fop is an index to show the optimization level of synonymous codon usage choice. It is basically a ratio of optimal codons against all codons used. The value of Fop ranges from 0 (no optimal codons are used) and 1 (only optimal codons are used). 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 gfop % gfop refseqn:NC_000913 Calculate the frequency of optimal codons (Fop) Codon usage output file [nc_000913.gfop]: 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 [*.gfop] Codon usage output file Additional (Optional) qualifiers: (none) Advanced (Unprompted) qualifiers: -translate boolean [N] Include when translates using standard codon table -[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 gfop reads one or more nucleotide sequences. Output file format The output from gfop is to a plain text file. File: nc_000913.gfop Sequence: NC_000913 Laa,Lc,fop,gene 20,5,0.4000,thrL 819,133,0.4361,thrA 309,46,0.4783,thrB 427,69,0.5217,thrC 97,7,0.2857,yaaX 257,56,0.4643,yaaA 475,96,0.3958,yaaJ 316,56,0.6964,talB [Part of this file has been deleted for brevity] 169,27,0.2593,yjjX 214,23,0.5652,ytjC 288,49,0.4082,rob 156,23,0.3478,creA 228,26,0.3462,creB 473,69,0.3478,creC 449,70,0.3286,creD 237,46,0.6957,arcA 45,10,0.7000,yjjY 227,24,0.2500,yjtD Data files None. Notes None. References Ikemura, T. (1981) Correlation between the abundance of Escherichia coli transfer RNAs and the occurrence of the respective codons in its protein genes: a proposal for a synonymous codon choice that is optimal for the E. coli translational system, J.Mol.Biol, 151:389-409. Ikemura (1985) Codon usage and tRNA content in unicellular and multicellular organisms, Mol.Biol.Evol, 2(1):13-34. 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) gscs Calculates the scaled chi-square gwvalue Calculate the 'relative adaptiveness of each codon' (W) 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.