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BP_REVTRANS-MOTIF(1) User Contributed Perl Documentation BP_REVTRANS-MOTIF(1) NAME bp_revtrans-motif - Reverse translate a Profam-like protein motif VERSION Version 0.01 SYNOPSIS From a file: bp_revtrans-motif.pl -i motifs.txt Using pipes: bp_revtrans-motif.pl < motifs.txt > output.txt Using interactively at the command prompt: $ bp_revtrans-motif.pl MAAEEL[VIKP] 1. ATGGCNGCNGARGARYTNVHN [^P]H(IW){2,3} 2. NDNCAY(ATHTGG){2,3} DESCRIPTION This 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 = All OPTIONS -i input-file: A file with a list of motifs to reverse translate. -h Display this help message. AUTHOR Bruno Vecchi, "vecchi.b at gmail.com" BUGS Please 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 v5.36.3 2021-02-03 BP_REVTRANS-MOTIF(1)
NAME | VERSION | SYNOPSIS | DESCRIPTION | OPTIONS | AUTHOR | BUGS | COPYRIGHT & LICENSE
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