diff GEMBASSY-1.0.3/doc/text/greporiter.txt @ 2:8947fca5f715 draft default tip

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--- a/GEMBASSY-1.0.3/doc/text/greporiter.txt	Fri Jun 26 05:20:29 2015 -0400
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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.
-