Mercurial > repos > ktnyt > gembassy
diff GEMBASSY-1.0.3/doc/text/gfindoriter.txt @ 2:8947fca5f715 draft default tip
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| author | ktnyt |
|---|---|
| date | Fri, 26 Jun 2015 05:21:44 -0400 |
| parents | 84a17b3fad1f |
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--- a/GEMBASSY-1.0.3/doc/text/gfindoriter.txt Fri Jun 26 05:20:29 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,189 +0,0 @@ - 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 (celery@g-language.org) - Institute for Advanced Biosciences, Keio University - 252-0882 Japan - - Kazuharu Arakawa (gaou@sfc.keio.ac.jp) - 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. -