bp_revtrans-motifp - Online in the Cloud

PROGRAM:

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.

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