NAME
glam2format - converts GLAM2 motifs to FASTA or MSF format
SYNOPSIS
glam2format [options] my_format my_motif.glam2
Formats: fasta, msf.
DESCRIPTION
glam2format reads in a motif found by glam2, and writes it in a
standard alignment format (FASTA-with-gaps or MSF). This enables the
alignment to be passed to third-party software, including graphical
visualization tools such as Kalignvu, Boxshade, and WebLogo. On the
other hand, not all the motif information is preserved: in particular,
the key positions are lost. Only the top motif in glam2 output is
converted.
OPTIONS (DEFAULT SETTINGS)
-o
Output file (stdout).
-c
Make a compact alignment. By default, residues that are inserted
between key positions are written as unaligned with each other.
This best reflects glam2´s intention, but it can make the alignment
large and full of gaps. With -c, inserted residues are written as
arbitrarily aligned with each other, just as they appear in the
glam2 output.
-f
Sequence file to make a “global” alignment by adding flanking
sequences from the original FASTA-format sequence file. The
flanking sequences will be written as either unaligned with each
other or arbitrarily aligned, depending on the -c option. The
sequences should have unique names and their order should be
unchanged.
SEE ALSO
boxshade(1), glam2(1), glam2mask(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.