revtrans-motif

Reverse translate a Profam-like protein motif

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

Dependencies

This module depends on the following:

• Test::More
• List::MoreUtils
• Bio::Tools::CodonTable
• Bio::Seq
• Pod::Usage
• Getopt::Long
• Sub::Exporter

Installation

To install this module, run the following commands:

perl Makefile.PL
make
make test
make install

Support and Documentation

After installing, you can find documentation for this module with the perldoc command.

perldoc revtrans-motif

Copyright and Licence

Copyright (C) 2009 Bruno Vecchi

This program is free software; you can redistribute it and/or modify it under the same terms as Perl itself.