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)
Check Out this Related Man Page
GLAM2MASK(1) glam2 Manual GLAM2MASK(1)NAME
glam2mask - masks a GLAM2 motif in sequences
SYNOPSIS
glam2mask [options] my_motif.glam2 my_seqs.fa
DESCRIPTION
glam2mask masks a glam2 motif out of sequences, so that weaker motifs can be found. Masking replaces residues aligned to key positions with
the symbol 'x'. By alternately applying glam2 and glam2mask several times, it is possible to find the strongest, second-strongest,
third-strongest, etc. motifs in a set of sequences.
OPTIONS (DEFAULT SETTINGS)-o
Output file (stdout).
-x
Mask character (x).
SEE ALSO glam2format(1), glam2(1), glam2-purge(1), glam2scan(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 GLAM2MASK(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)
Hi everyone, I am new in motif programming and I want to learn how to program it. I use Fedora core 3 and every time I compile the program, there are always some errors appear. One of the errors said that I do not have the Xm/xxxx.h However, I do not know precisely how to install header files. I... (0 Replies)
hello everyone,
where can i download motif compatible with HP-UX 11.11.which motif version i have to use.
can i use openmotif 2.3 for HP-UX 11.11.
pls somebody suggest a solution .it's very urgent.
any help appreciated.
with regards,
Srini (0 Replies)
Hi,
I need to find whether the first character in a line is a alphabet or a number. If its a number i should sort it numerically. If its a alphabet i should sort it based on the ASCII value.And if it is something other than alphabet or number then sort it based on ASCII value.
The code i used... (2 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)
afternoon forums.
I need to get a way of testing as to wether an inputed character is part of the english alphabet.
i have come up with the following code but its not working at all.
until ']
do
echo This is not a Letter
done
any help would be beneficial to me. (1 Reply)
Hi All,
We have a 32bit Motif Gui application. Now we ported the application from Solaris to Linux and the system is crashing very frequently. On our analysis we could find that this issue happened when we are closing the forms in our application. When the forms are closed we will delete the forms... (0 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)