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gdeltagcskew Function Calculate strand bias of bacterial genome using delta GC skew index Description gdeltagcskew calculates strand bias of bacterial genome using delta GC skew index, first proposed by Rocha et al. (2001), and further extended in 2006. Basic idea of delta GC skew index is to calculate the difference of GC skew in coding regions residing in leading and lagging strands. Rocha et al. (2001) calculates delta GC skew index using the third codon position of genes, and Rocha et al. (2006) modified to only use >fourfold degenerate codons. 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 gdeltagcskew % gdeltagcskew refseqn:NC_000913 Calculate strand bias of bacterial genome using delta GC skew index Program compseq output file [nc_000913.gdeltagcskew]: 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 [*.gdeltagcskew] Program compseq output file Additional (Optional) qualifiers: (none) Advanced (Unprompted) qualifiers: -at boolean [N] Include when observing AT skew instead of GC skew -purine boolean [N] Include when observing purine (AG/TC) skew -keto boolean [N] Include when observing keto (TG/AC) skew -method selection [degenerate] Choose the nucleotides to use 'degenerate', 'gc3', or 'all' -[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 gdeltagcskew reads one or more nucleotide sequences. Output file format The output from gdeltagcskew is to a plain text file. File: nc_000913.gdeltagcskew Sequence: NC_000913 DELTA-GCskew -0.108937 Data files None. Notes None. References Rocha EPC et al. (2001) Ongoing Evolution of Strand Composition in Bacterial Genomes, Molecular Biology and Evolution, 18(9):1789-1799 Rocha EPC et al. (2006) Similar compositional biases are caused by very different mutational effects, Genome Research, 16:1537-1547 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 ggcsi GC Skew Index: an index for strand-specefic mutational bias gldabias Calculate strand bias of bacterial genome using linear discriminant analysis (LDA) 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.