glam2format(1) [debian man page]

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)

GLAM2(1)							   glam2 Manual 							  GLAM2(1)

NAME

       glam2 - Gapped Local Alignment of Motifs

SYNOPSIS

       glam2 [options] alphabet my_seqs.fa

       An alphabet other than p or n is interpreted as the name of an alphabet file.

DESCRIPTION

       GLAM2 is a software package for finding motifs in sequences, typically amino-acid or nucleotide sequences. A motif is a re-occurring
       sequence pattern: typical examples are the TATA box and the CAAX prenylation motif. The main innovation of GLAM2 is that it allows
       insertions and deletions in motifs.

OPTIONS (DEFAULT SETTINGS)
       -h
	   Show all options and their default settings.

       -o
	   Output file (stdout).

       -r
	   Number of alignment runs (10).

       -n
	   End each run after this many iterations without improvement (10000).

       -2
	   Examine both strands - forward and reverse complement.

       -z
	   Minimum number of sequences in the alignment (2).

       -a
	   Minimum number of aligned columns (2).

       -b
	   Maximum number of aligned columns (50).

       -w
	   Initial number of aligned columns (20).

       -d
	   Dirichlet mixture file.

       -D
	   Deletion pseudocount (0.1).

       -E
	   No-deletion pseudocount (2.0).

       -I
	   Insertion pseudocount (0.02).

       -J
	   No-insertion pseudocount (1.0).

       -q
	   Weight for generic versus sequence-set-specific residue abundances (1e+99).

       -t
	   Initial temperature (1.2).

       -c
	   Cooling factor per n iterations (1.44).

       -u
	   Temperature lower bound (0.1).

       -p
	   Print progress information at each iteration.

       -m
	   Column-sampling moves per site-sampling move (1.0).

       -x
	   Site sampling algorithm: 0=FAST 1=SLOW 2=FFT (0).

       -s
	   Seed for pseudo-random numbers (1).

SEE ALSO

       glam2format(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								  GLAM2(1)