11-30-2019
Hello Sennenmut,
Good that you were able to solve the problem by your own. But after working on few posts in this thread and suddenly declaring that you have solved the problem will not help anyone.
I would like to request you to please do add your solution which helped you fix your problem in this thread do that future users could be benefited too. Cheers and happy learning on this great site.
Thanks,
R. Singh
This User Gave Thanks to RavinderSingh13 For This Post:
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LEARN ABOUT DEBIAN
glam2scan
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)