Man Linux: Main Page and Category List


       glam2format - converts GLAM2 motifs to FASTA or MSF format


       glam2format [options] my_format my_motif.glam2

       Formats: fasta, msf.


       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


           Output file (stdout).

           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.

           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


       boxshade(1), glam2(1), glam2mask(1), glam2-purge(1), glam2scan(1)

       The full Hypertext documentation of GLAM2 is available online at or on this computer in


       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).


       Martin Frith
           Author of GLAM2.

       Timothy Bailey
           Author of GLAM2.

       Charles Plessy <>
           Formatted this manpage in DocBook XML for the Debian distribution.


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