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