diff 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.
+