GLAM2FORMAT(1) glam2 Manual GLAM2FORMAT(1)
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.
GLAM2 1056 05/19/2008 GLAM2FORMAT(1)