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| author | ktnyt |
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| date | Fri, 26 Jun 2015 05:20:29 -0400 |
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gldabias Function Calculate strand bias of bacterial genome using linear discriminant Description gldabias calculates strand bias of bacterial genome using linear discriminant analysis (LDA), as proposed in Reference 1. The basic idea is to use composition data of genes to train and predict the strand of genes residing either on the leading or the lagging strand. For computational efficiency, this method trans and predicts the strands at putative replication origin as reported by the rep_ori_ter() method. This usually results in maximum predictability of LDA within bacterial genomes. Data to use for LDA can be chosen from "base", "codonbase", "codon", and "amino", with -variable option. 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 gldabias % gldabias refseqn:NC_000913 Calculate strand bias of bacterial genome using linear discriminant analysis (LDA) Program compseq output file [nc_000913.gldabias]: Go to the input files for this example Go to the output files for this example Command line arguments Calculate strand bias of bacterial genome using linear discriminant analysis (LDA) Version: EMBOSS:6.5.7.0 GEMBASSY:1.0.1 Standard (Mandatory) qualifiers: [-sequence] seqall Nucleotide sequence(s) filename and optional format, or reference (input USA) [-outfile] outfile [*.gldabias] Program compseq output file Additional (Optional) qualifiers: (none) Advanced (Unprompted) qualifiers: -coefficients integer [0] Show LDA coefficients (Any integer value) -variable selection [codon] Data to use for LDA. Either 'base', 'codonbase', 'codon', or 'amino' -[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 gldabias reads one or more nucleotide sequences. Output file format The output from gldabias is to a plain text file. File: nc_000913.gldabias Sequence: NC_000913 LDA-BIAS: 0.742533 Data files None. Notes None. References Rocha EPC et al. (1999) "Universal replication biases in bacteria", Molecular Microbiology, 32(1):11-16 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 gb1 Calculate strand bias of bacterial genome using B1 index gb2 Calculate strand bias of bacterial genome using B2 index gdeltagcskew Calculate strand bias of bacterial genome using delta GC skew index ggcsi GC Skew Index: an index for strand-specefic mutational bias 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.