bp_revtrans-motif1p
Reverse translate a profam-like protein motif
Usage
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:
MAAEEL [VIKP]
1. ATGGCNGCNGARGARYTNVHN
[^P]
H(IW)
2,3
2. NDNCAY(ATHTGG)
2,3
Version
Version 0.01
Overview
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
normtimes. 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 + DZ = Q + EX = All
Options
-i input-file:
A file with a list of motifs to reverse translate.
-h
Display this help message.
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.
Releases
8 releases since Debian 6.0 (Squeeze); the text changed 6 times.