This is the command glam2scan that can be run in the OnWorks free hosting provider using one of our multiple free online workstations such as Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator
PROGRAM:
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.
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