BP_REVTRANS-MOTIF(1) User Contributed Perl Documentation BP_REVTRANS-MOTIF(1)NAME
revtrans-motif - Reverse translate a Profam-like protein motif
VERSION
Version 0.01
SYNOPSIS
From 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}
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 v5.14.1 2011-07-22 BP_REVTRANS-MOTIF(1)