1BP_REVTRANS-MOTIF(1)  User Contributed Perl Documentation BP_REVTRANS-MOTIF(1)
2
3
4

NAME

6       revtrans-motif - Reverse translate a Profam-like protein motif
7

VERSION

9       Version 0.01
10

SYNOPSIS

12       From a file:
13
14           revtrans-motif.pl -i motifs.txt
15
16       Using pipes:
17
18          revtrans-motif.pl < motifs.txt > output.txt
19
20       Using interactively at the command prompt:
21
22          $ revtrans-motif.pl
23          MAAEEL[VIKP]
24          1.   ATGGCNGCNGARGARYTNVHN
25          [^P]H(IW){2,3}
26          2.   NDNCAY(ATHTGG){2,3}
27

DESCRIPTION

29       This script takes a protein motif as input and returns a degenerate
30       oligonucleotide sequence corresponding to it. The main reason for doing
31       this is to design degenerate primers that amplify a given sequence
32       pattern.
33
34       The input motif consists of a string of one-letter residues, with any
35       of the following syntactic elements:
36
37       [...] : Redundant position.
38           A position in which more than one residue is allowed. Example:
39
40               [TS]YW[RKSD]
41                ^^    ^^^^
42
43       [^...] : Negated position.
44           A position in which any residue is allowed, saved for those between
45           brackets. Example:
46
47               [^PW]MK[LAE]
48                 ^^
49
50       (...){n,m,...} : Repeated motif.
51           A motif that is repeated n or m times. It can have any of the
52           previous syntactic elements. Example:
53
54               A[SN]C(TXX){2,4,8}
55                      ^^^
56
57       The allowed letters are those that correspond to the 20 natural
58       aminoacids, plus:
59
60           B = N + D
61           Z = Q + E
62           X = All
63

OPTIONS

65   -i input-file:
66       A file with a list of motifs to reverse translate.
67
68   -h
69       Display this help message.
70

AUTHOR

72       Bruno Vecchi, "vecchi.b at gmail.com"
73

BUGS

75       Please report any bugs or feature requests to "vecchi.b at gmail.com"
76

78       Copyright 2009 Bruno Vecchi, all rights reserved.
79
80       This program is free software; you can redistribute it and/or modify it
81       under the same terms as Perl itself.
82
83
84
85perl v5.12.0                      2010-04-29              BP_REVTRANS-MOTIF(1)
Impressum