Mercurial > repos > ktnyt > gembassy
diff GEMBASSY-1.0.3/doc/text/gconsensusz.txt @ 0:8300eb051bea draft
Initial upload
| author | ktnyt |
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| date | Fri, 26 Jun 2015 05:19:29 -0400 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/GEMBASSY-1.0.3/doc/text/gconsensusz.txt Fri Jun 26 05:19:29 2015 -0400 @@ -0,0 +1,205 @@ + gconsensusz +Function + + Calculate consensus in given array of sequences + +Description + + gconsensusz calculates the consensus of given list of sequences, using + Z-score. The Z-score will show higher values when the sequences are biased + to a single character within the list. + + 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 gconsensusz + +% gconsensusz consensus.fasta +Calculate consensus in given array of sequences +Program compseq output file (optional) [rs_000000.gconsensusz]: + + Go to the input files for this example + Go to the output files for this example + + Example 2 + +% gconsensusz consensus.fasta -plot -graph png +Calculate consensus in given array of sequences +Created gconsensusz.1.png + + Go to the input files for this example + Go to the output files for this example + +Command line arguments + + Standard (Mandatory) qualifiers (* if not always prompted): + [-sequence] seqall Nucleotide sequence(s) filename and optional + format, or reference (input USA) +* -graph xygraph [$EMBOSS_GRAPHICS value, or x11] Graph type + (ps, hpgl, hp7470, hp7580, meta, cps, x11, + tek, tekt, none, data, xterm, png, gif, svg) +* -outfile outfile [*.gconsensusz] Program compseq output file + (optional) + + Additional (Optional) qualifiers: (none) + Advanced (Unprompted) qualifiers: + -high integer [1] Z value greater than which is + significant (Any integer value) + -low float [0.2] Z value less than which is + insignificant (Any numeric value) + -plot toggle [N] Include to plot result + + 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 + + "-graph" associated qualifiers + -gprompt boolean Graph prompting + -gdesc string Graph description + -gtitle string Graph title + -gsubtitle string Graph subtitle + -gxtitle string Graph x axis title + -gytitle string Graph y axis title + -goutfile string Output file for non interactive displays + -gdirectory string Output directory + + "-outfile" associated qualifiers + -odirectory 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 + + gconsensusz reads one or more nucleotide sequences. + +Output file format + + The output from gconsensusz is to a plain text file or the EMBOSS graphics device. + + File: rs_000000.gconsensusz + 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+ + +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 + + gdistincc Calculates the distance between two loci in circular chromosomes + gpalindrome Searches palindrome sequences + gseqinfo Prints out basic nucleotide sequence statistics + +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. +