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.