comparison GEMBASSY-1.0.3/doc/text/greporiter.txt @ 0:8300eb051bea draft

Initial upload

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                                   greporiter
Function

   Get the positions of replication origin and terminus

Description

   greporiter returns the positions of replication origin and terminus
   in bacterial genomes by several means. 

   1. Use of databases
   By default, grep_ori_ter tries to retrieve the position of replication
   origin in DoriC Gao and Zhang (2007) database, and the position of
   replication terminus from the supplemental data provided in
   Kono et al. (2011).
   If the position of origin cannot be found in the database, but "rep_origin" 
   feature is available, center position within this feature is used for
   origin. 

   2. Oriloc
   Using -orilocoption, you can predict the replication origin and 
   terminus using the popular Oriloc program developed by Lobry et al. 
   available as part of the SeqinR package Frank and Lobry (2000).

   3. Use GC skew shift-point
   If the positions of origin or terminus cannot be found in the databases,
   grep_ori_ter automatically calls find_ori_ter() method to predict the 
   positions using GC skew shift-points at one-base-pair resolution.
    
   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 greporiter

% greporiter refseqn:NC_000913
Get the positions of replication origin and terminus
Output file [nc_000913.greporiter]: 

   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    [*.greporiter] Output file name

   Additional (Optional) qualifiers: (none)
   Advanced (Unprompted) qualifiers:
   -oriloc             boolean    [N] Include Oriloc for prediction
   -gcskew             boolean    [N] Include to use GC skew shift-point for
                                  prediction
   -difthreshold       integer    [0] Distance between the GC skew shift point
                                  and predicted dif site expressed as the
                                  precentage of genome size, used as a
                                  threshold to retrieve dif sequence from the
                                  database (Any integer value)
   -dbonly             boolean    [N] Include to only use values available in
                                  databases and to suppress prediction
   -[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

   greporiter reads one or more nucleotide sequences.

Output file format

   The output from greporiter is to a plain text file.

   File: nc_000913.greporiter

Sequence: NC_000913 Origin: 3923881 Terminus: 1550412


Data files

   None.

Notes

   None.

References

   Gao F and Zhang CT (2007) DoriC: a database of oriC regions in bacterial
      genomes, Bioinformatics, 23(14):1866-1867

   Kono N et al. (2011) Comprehensive prediction of chromosome dimer resolution 
      sites in bacterial genomes, BMC Genomics, 12(1):19

   Frank AC and Lobry JR (2000) "Oriloc: prediction of replication boundaries 
      in unannotated bacterial chromosomes", Bioinformatics, 16(6):560-561

   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

   gfindoriter Predicts the replication origin and terminus in bacterial
               genomes

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.