Package: revtrans
NAMErevtrans - performs a reverse translation of a peptide alignmentSYNOPSISrevtrans dnafile pepfile [-v] [-h] [-gapin chars] [-gapout char][-Idna format] [-Ipep format] [-mtx tablename/file] [-match method][-O format] [outfile]DESCRIPTIONReads a set of aligned peptide sequences from pepfile and usesthe corresponding DNA sequences from dnafile to construct areverse translated version of the alignment.By default the input file formats are auto detected and thecorresponding DNA and peptide sequences is found by translation.In the typical case this means that the user only need tosupply the DNA and peptide sequences, and may safely ignorethe more advanced options. E.g :revtrans kinases.dna.fsa kinases.prot.alnThe final alignment is written to STDOUT or outfile if specified,and is by default in FASTA format.OPTIONS-hHelp. Print this help information.-gapin charsSpecify gap characters in the input sequences.Default is '.-~'-gapout	charSpecify which character should be used for gaps in theoutput.Default is '-'-Idna formatSpecify format of the input DNA file.Valid formats are: auto (default), fasta, msf and aln-Ipep formatSpecify format of the input peptide file.Valid formats are: auto (default), fasta, msf and aln-O formatSpecify format of the output file.Valid formats are: fasta (default), msf and aln-mtx tablename/fileUse alternative translation matrix instead of the build-inStandard Genetic Code for translation.If "tablename" is 1-6,9-16 or 21-23 one of the alternativetranslation tables defined by the NCBI taxonomy group will beused.Briefly, the following tables are defined:-----------------------------------------1: The Standard Code2: The Vertebrate Mitochondrial Code3: The Yeast Mitochondrial Code4: The Mold, Protozoan, and Coelenterate Mitochondrial Codeand the Mycoplasma/Spiroplasma Code5: The Invertebrate Mitochondrial Code6: The Ciliate, Dasycladacean and Hexamita Nuclear Code9: The Echinoderm and Flatworm Mitochondrial Code10: The Euplotid Nuclear Code11: The Bacterial and Plant Plastid Code12: The Alternative Yeast Nuclear Code13: The Ascidian Mitochondrial Code14: The Alternative Flatworm Mitochondrial Code15: Blepharisma Nuclear Code16: Chlorophycean Mitochondrial Code21: Trematode Mitochondrial Code22: Scenedesmus obliquus mitochondrial Code23: Thraustochytrium Mitochondrial CodeSee http://www.ncbi.nlm.nih.gov/Taxonomy [Genetic Codes]for a detailed description. Please notice that the tableof start codons is also used (see the -allinternal optionbelow for details).If a filename is supplied the translation table is read fromfile instead.The file should contain one line per codon in the format:codon<whitespace>aa-single letter codeAll 64 codons must be included. Stop codons is specifiedby "*". T and U is interchangeable. Blank lines and linesstarting with "#" are ignored.See the "gcMitVertebrate.mtx" file in the RevTrans sourcedistribution for a well documented example.-allinternalBy default the very first codon in each sequences is assumedto be the initial codon on the transcript. This means certainnon-methionine codons actually codes for metionine at thisposition. For example "TTG" in the standard genetic code (seeabove).Selecting this option treats all codons as internal codons.-readthroughstopAllow the translation to continue after a stop codon is reached.The stop codon will be marked as "*".Be careful that stop codons have been addressed in the same mannerin the input peptide alignment.-match methodSpecify how to match the corresponding DNA and peptidesequences. Valid methods are: trans (default), name and pos.Please note that both DNA and peptide sequence should haveunique names, regardless of the matching method.trans:Match sequences by translation. The DNA sequences aretranslated using the standard genetic code (default)or an alternative translation matrix if the -mtxoption is used.name:Match sequences by name. Please note that for FASTAfiles everything after the ">" is considered thesequence name.pos:Match by position. The sequence are matched by positionin the files (first DNA sequence with first peptidesequence etc.).-vVerbose. Print extra information about files, sequencesand the progress in general to STDERR.The verbose level can be set to three degrees ofdetail.-v:   verbose level 1Info about files, number of sequences read etc.Use this as the first try if something needsinvestigation.-vv:  verbose level 2As level 1 +Print detailed info about all the sequence names.-vvv: verbose level 3As level 2 +Do a sanity check on the degapped length of thesequences. Warn if the sizes do not match.AUTHORRasmus Wernersson, raz@cbs.dtu.dkSeptember 2002, February 2003, July 2004, April 2005FILESrevtrans.py, mod_translate.py, mod_seqfiles.py,ncbi_genetic_codes.pyWEB PAGEhttp://www.cbs.dtu.dk/services/RevTrans/REFERENCERasmus Wernersson and Anders Gorm Pedersen.RevTrans - Constructing alignments of coding DNA from aligned aminoacid sequences.Nucl. Acids Res., 2003, 31(13), 3537-3539.