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This is the command bp_revtrans-motifp that can be run in the OnWorks free hosting provider using one of our multiple free online workstations such as Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator

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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