bp_revtrans-motif - Reverse translate a Profam-like protein motif
Version 0.01
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}
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:
A position in which more than one residue is allowed. Example:
[TS]YW[RKSD] ^^ ^^^^
A position in which any residue is allowed, saved for those between brackets. Example:
[^PW]MK[LAE] ^^
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
A file with a list of motifs to reverse translate.
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Bruno Vecchi, vecchi.b at gmail.com
vecchi.b at gmail.com
Please report any bugs or feature requests to vecchi.b at gmail.com
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.
To install Bio::Seq, copy and paste the appropriate command in to your terminal.
cpanm
cpanm Bio::Seq
CPAN shell
perl -MCPAN -e shell install Bio::Seq
For more information on module installation, please visit the detailed CPAN module installation guide.