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glam2scan

Langue: en

Version: 05/19/2008 (debian - 07/07/09)

Section: 1 (Commandes utilisateur)

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.

The source code and the documentation of GLAM2 are released in the public domain.

En amour, les femmes écrivent des choses qu'elles ne diraient pas,
et le hommes disent des choses qu'ils n'écriraient pas.
-+- François René de Chateaubriand -+-