Query: bp_revtrans-motif
OS: debian
Section: 1p
Format: Original Unix Latex Style Formatted with HTML and a Horizontal Scroll Bar
BP_REVTRANS-MOTIF(1p) User Contributed Perl Documentation BP_REVTRANS-MOTIF(1p)NAMErevtrans-motif - Reverse translate a Profam-like protein motifVERSIONVersion 0.01SYNOPSISFrom a file: revtrans-motif.pl -i motifs.txt Using pipes: revtrans-motif.pl < motifs.txt > output.txt Using interactively at the command prompt: $ revtrans-motif.pl MAAEEL[VIKP] 1. ATGGCNGCNGARGARYTNVHN [^P]H(IW){2,3} 2. NDNCAY(ATHTGG){2,3}DESCRIPTIONThis script takes a protein motif as input and returns a degenerate oligonucleotide sequence corresponding to it. The main reason for doing this is to design degenerate primers that amplify a given sequence pattern. The input motif consists of a string of one-letter residues, with any of the following syntactic elements: [...] : Redundant position. A position in which more than one residue is allowed. Example: [TS]YW[RKSD] ^^ ^^^^ [^...] : Negated position. A position in which any residue is allowed, saved for those between brackets. Example: [^PW]MK[LAE] ^^ (...){n,m,...} : Repeated motif. A motif that is repeated n or m times. It can have any of the previous syntactic elements. Example: A[SN]C(TXX){2,4,8} ^^^ The allowed letters are those that correspond to the 20 natural aminoacids, plus: B = N + D Z = Q + E X = AllOPTIONS-i input-file: A file with a list of motifs to reverse translate. -h Display this help message.AUTHORBruno Vecchi, "vecchi.b at gmail.com"BUGSPlease report any bugs or feature requests to "vecchi.b at gmail.com" COPYRIGHT & LICENSE Copyright 2009 Bruno Vecchi, all rights reserved. This program is free software; you can redistribute it and/or modify it under the same terms as Perl itself. perl v5.14.2 2012-03-02 BP_REVTRANS-MOTIF(1p)