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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 converted.


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 unchanged.

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