glam2mask(1) [debian man page]

GLAM2MASK(1)							   glam2 Manual 						      GLAM2MASK(1)

NAME

       glam2mask - masks a GLAM2 motif in sequences

SYNOPSIS

       glam2mask [options] my_motif.glam2 my_seqs.fa

DESCRIPTION

       glam2mask masks a glam2 motif out of sequences, so that weaker motifs can be found. Masking replaces residues aligned to key positions with
       the symbol 'x'. By alternately applying glam2 and glam2mask several times, it is possible to find the strongest, second-strongest,
       third-strongest, etc. motifs in a set of sequences.

OPTIONS (DEFAULT SETTINGS)
       -o
	   Output file (stdout).

       -x
	   Mask character (x).

SEE ALSO

       glam2format(1), glam2(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.

GLAM2 1056							    05/19/2008							      GLAM2MASK(1)

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.

GLAM2 1056							    05/19/2008							    GLAM2FORMAT(1)