annotate GEMBASSY-1.0.3/doc/text/gbasezvalue.txt @ 0:8300eb051bea draft

Initial upload

                                  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 ([e-mail])
   Institute for Advanced Biosciences, Keio University
   252-0882 Japan

   Kazuharu Arakawa ([e-mail])
   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.