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

Initial upload

                                  gfindoriter
Function

   Predict the replication origin and terminus in bacterial genomes

Description

   gfindoriter predicts the replicational origin and terminus in circular
   bacterial genomes, by taking the vertices of cumulative skew graphs (GC,
   d keto, or purine). See Frank and Lobry (2000) for the basic idea behind
   this algorithm (but also note that this algorithm is different from that
   of Oriloc, which uses GC3 of genes). 
   Terminus of replication can be more accurate by using noise-reduction 
   filtering using Fourier spectrum of the GC skew. This low-pass filtering
   can be applied using -filter option. See Arakawa et al. (2007) for details.
    
   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 gfindoriter

% gfindoriter refseqn:NC_000913
Predict the replication origin and terminus in bacterial genomes
Output file [nc_000913.gfindoriter]: 

   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    [*.gfindoriter] Output file name

   Additional (Optional) qualifiers: (none)
   Advanced (Unprompted) qualifiers:
   -window             integer    [4096] Number of windows to use for Fat
                                  Fourier Transform. Only active when -lowpass
                                  option is specified. Value must be the
                                  power of two (Any integer value)
   -purine             boolean    [N] Use purine skew for calculation
   -keto               boolean    [N] Use keto skew for calculation
   -lowpass            integer    [0] Lowpass filter strength in percent.
                                  Typically 95 or 99 works best (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

   gfindoriter reads one or more nucleotide sequences.

Output file format

   The output from gfindoriter is to a plain text file.

   File: nc_000913.gfindoriter

Sequence: NC_000913 Origin: 3922946 Terminus: 1550274


Data files

   None.

Notes

   None.

References

   Frank AC, Lobry JR (2000) Oriloc: prediction of replication boundaries in
      unannotated bacterial chromosomes, Bioinformatics, 16:566-567.

   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

   greporiter Gets the positions of replication origin and terminus

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.