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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.

05/19/2008 GLAM2 1056