This is the command glam2format that can be run in the OnWorks free hosting provider using one of our multiple free online workstations such as Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator
PROGRAM:
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.
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