BP_REVTRANS-MOTIF(1p) User Contributed Perl Documentation BP_REVTRANS-MOTIF(1p)NAME
revtrans-motif - Reverse translate a Profam-like protein motif
VERSION
Version 0.01
SYNOPSIS
From a file:
revtrans-motif.pl -i motifs.txt
Using pipes:
revtrans-motif.pl < motifs.txt > output.txt
Using interactively at the command prompt:
$ 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.
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.
perl v5.14.2 2012-03-02 BP_REVTRANS-MOTIF(1p)
Check Out this Related Man Page
GLAM2SCAN(1) glam2 Manual GLAM2SCAN(1)NAME
glam2scan - finds a GLAM2 motif in a database
SYNOPSIS
glam2scan [options] alphabet my_motif.glam2 my_seqs.fa
An alphabet other than p or n is interpreted as the name of an alphabet file.
DESCRIPTION
glam2scan finds matches, in a sequence database, to a motif discovered by glam2. Each match receives a score, indicating how well it fits
the motif.
OPTIONS (DEFAULT SETTINGS)-h
Show all options and their default settings.
-o
Output file (stdout).
-n
Number of alignments to report (25).
-2
Examine both strands - forward and reverse complement.
-D
Deletion pseudocount (0.1).
-E
No-deletion pseudocount (2.0).
-I
Insertion pseudocount (0.02).
-J
No-insertion pseudocount (1.0).
-d
Dirichlet mixture file.
SEE ALSO glam2format(1), glam2mask(1), glam2-purge(1), glam2(1)
The full Hypertext documentation of GLAM2 is available online at http://bioinformatics.org.au/glam2/ or on this computer in
/usr/share/doc/glam2/.
REFERENCE
If you use GLAM2, please cite: MC Frith, NFW Saunders, B Kobe, TL Bailey (2008) Discovering sequence motifs with arbitrary insertions and
deletions, PLoS Computational Biology (in press).
AUTHORS
Martin Frith
Author of GLAM2.
Timothy Bailey
Author of GLAM2.
Charles Plessy <plessy@debian.org>
Formatted this manpage in DocBook XML for the Debian distribution.
COPYRIGHT
The source code and the documentation of GLAM2 are released in the public domain.
GLAM2 1056 05/19/2008 GLAM2SCAN(1)
Can somebody help me...
I have insalled RedHat 7.3 on my computer
and there is motif 2.x and i want to compile a cource code but it doesn't work it says
Xm/PushB.h not found..something like that..
I'm trying like this :
gcc -o x x.c -lXm -lXt -lX11
pleas help me (3 Replies)
I have files coming to an input directory every few mins...eg
test_00012.txt
test_00013.txt
test_00014.txt
I need to write a script to monitor these and if a file is missing from the sequence I need my script to spot this so I can alert someone...
ie... if I got the following:... (1 Reply)
I hope I am posting this in the right section.
I have c file that is using the motif GUI toolkit to draw widgets and things of that sort. I also have another program that runs with xnest. I need to figure out a way to place that xnest program in my c code so that it exists in the window that the... (4 Replies)
Hello every one,
i am attempting to install motif on HP-UX 11.11 ,which motif version i have to use for installation &where can i get that motif versin.
pls provide the information like websites which are containing open motif to install it on HP-UX 11.11.
IT'S VERY URGENT.
any help... (3 Replies)
Hi All the Helpers!
I have a text file which looks like input.txt.I would request to please suggest me how can I make this file look like output.txt
input.txt
VOP 111 0 1 2
DEM 111 0 222 333 444 555
DEM 879 888 987 888 989
DEM 879 888 987 888 989
VOP 118 0 12 3 6... (7 Replies)
Hi all,
I am using following command:
perl program.pl input.txt output.txt CUTOFF 3 > groups_3.txt
containing program.pl, two files (input.txt, output.txt) and getting output in groups_3.txt:
But, I wish to have 30 files corresponding to each CUTOFF ranging from 0 to 30 using the same... (1 Reply)
Hi friends,
I am pretty new to shell scripting, please help me in this Scenario.
for example, If I have one file called input.txt
once I run the script,
1.It has to delete the old input.txt and create the new input.txt (if old input.txt is not there, no offence, just it has to create a... (2 Replies)
I have two files
1. input.txt
2. keyword.txt
input.txt has contents like
.src_ref 0 "call.s" 24 first
0x000000 0x5a80 0x0060 BRA.l 0x60
.src_ref 0 "call.s" 30 first
0x000002 0x1bc5 RETI
.src_ref 0 "call.s" 31 first
0x000003 0x6840 ... (2 Replies)
Hi there ,
i am interesting in MOTIF programming.
One question :
Is it right that in Motif GUI programming the actions are automaticly transformed and networked to other clients over the internet without network programming necessary ?
Are the commands automatic transformed by the X11... (4 Replies)
Hi there. :)
I found MOTIF programming code with file dialogs.
In the compiling description is the speak of a Libarary PW.
This compiling description is mentioned :
gcc -o newone test.c -lXm -lXt -lX11 -lPW
Has anyone heared about that Library. ?
After compiling GCC is asking for... (4 Replies)
MOTIF GUI PROGRAMMING !
Hi there. I am a MOTIF GUI Programmer in C language.
After a longer break i have problems with the GCC compiling.
my MOTIF file is named winstack.c
I have the follow code gcc -o newprogram winstack.c -lXm -lXt -lX11
The compilation runs good.
But no executable LINUX... (10 Replies)
Hi,
i have here found a very good texteditor source code programmed in the MOTIF GUI language.
For myself i need NOTHING else to program.
To start from a very easy point of view i want to RUN this editor on my LINUX machine and type simple C code.
The reason for this post is that the text... (7 Replies)
Hello,
i have installed open-motif -2.3.8_1 X11 Toolkit on freebsd32bit machine.
wanna compile a little script. script is ok. already compiled on other machine (linux)
the message is as follows
cc -o button button.c -lXm -lXt -lX11
button.c:3:10: fatal error: 'Xm/Xm.h' file not found... (5 Replies)