Man page - bp_revtrans-motif(1)
Packages contains this manual
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- bp_revtrans-motif(1)
- bp_mask_by_search(1)
- bp_seqcut(1)
- bp_mrtrans(1)
- bp_seqret(1)
- bp_filter_search(1)
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- bp_seqconvert(1)
- bp_search2gff(1)
- bp_bioflat_index(1)
- bp_oligo_count(1)
- bp_search2table(1)
- bp_genbank2gff3(1)
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- bp_local_taxonomydb_query(1)
- bp_fetch(1)
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apt-get install bioperl
Manual
BP_REVTRANS-MOTIF
NAMEVERSION
SYNOPSIS
DESCRIPTION
OPTIONS
-i input-file:
-h
AUTHOR
BUGS
COPYRIGHT & LICENSE
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
[ˆP]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]
ˆˆ ˆˆˆˆ
[ˆ...] : Negated position.
A position in which any residue is allowed, saved for those between brackets. Example:
[ˆPW]MK[LAE]
ˆˆ
(...){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}
ˆˆˆ
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.