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| author | ktnyt |
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| date | Fri, 26 Jun 2015 05:19:29 -0400 |
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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.