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| author | ktnyt |
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| date | Fri, 26 Jun 2015 05:19:29 -0400 |
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gbasezvalue Function Extracts conserved oligomers per position using Z-score Description This function calculates and extracts conserved oligomers per position using Z-score, in regions around the start/stop codons. The oligomers are returned in ranking order up to "-limit" number. The Z-score for mean m and standard error SE is calculated as follows: z = (x - m) / SE where SE for standard deviation s and number of samples s is as follows: SE = s/sqrt(n) 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 gbasezvalue % gbasezvalue refseqn:NC_000913 Extracts conserved oligomers per position using Z-score Program compseq output file (optional) [nc_000913.gbasezvalue]: 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 [*.gbasezvalue] Program compseq output file (optional) Additional (Optional) qualifiers: (none) Advanced (Unprompted) qualifiers: -limit integer [5] Rank threshold for showing the conserved oligomer (Any integer value) -position selection [start] Either 'start' (around start codon) or 'end' (around stop codon) to create the PWM -patlen integer [3] Length of oligomer to count (Any integer value) -upstream integer [30] Length upstream of specified position to create PWM (Any integer value) -downstream integer [30] Length downstream of specified position to create PWM (Any integer value) -[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 gbasezvalue reads one or more nucleotide sequences. Output file format The output from gbasezvalue is to a plain text file. File: nc_000913.gbasezvalue Sequence: NC_000913 position:-30,1,taa,-0.76525 2,aga,-0.79101 3,tta,-1.14174 4,cta,-1.18831 5,aat,-1.86652 position:-29,1,cta,-0.18368 2,aat,-0.71851 3,gac,-1.26182 4,taa,-1.39455 [Part of this file has been deleted for brevity] position:29,1,gct,1.66288 2,act,1.26637 3,tat,0.66721 4,cct,-0.43158 5,tgt,-0.59254 position:30,1,ctg,3.12072 2,att,0.04193 3,ctc,-0.12416 4,cta,-0.38461 5,tta,-0.76413 Data files None. Notes None. References 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 gbasecounter Creates a position weight matrix of oligomers around start codon gviewcds Displays a graph of nucleotide contents around start and stop codons 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.