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.