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)

Check Out this Related Man Page

SQUIZZ(1)							   User Manuals 							 SQUIZZ(1)

NAME

       squizz - Sequence format checker

SYNOPSIS

       squizz [-AShlns] [-c format] [-f format] file

OPTIONS

       Following command line options are allowed:

       -A  Restrict detection/verification to alignment formats (conflict with -S option).

       -S  Restrict detection/verification to sequence formats (conflict with -A option).

       -c format
	   Convert detected sequence/alignment into format. This option implies strict alignment checking.

       -f format
	   Assume input format is format. Do not try to detect the format, just verify that the given one is correct.

       -h  Usage display.

       -l  List all supported formats.

       -n  Count and report detected entries. This option is only available when the detection is restricted to a single type (with -A or -S
	   options) and strict checks (without -s option) are enabled.

       -s  Disable strict format checks (enabled by default).

DESCRIPTION

       squizz is a sequence format file checker, but it has some conversion capabilities too.

       squizz can detect the most common sequence and alignment formats :

       * EMBL, FASTA, GCG, GDE, GENBANK, IG, NBRF, PIR (codata), RAW, and SWISSPROT.

       * CLUSTAL, FASTA, MSF, NEXUS, PHYLIP (interleaved and sequential) and STOCKHOLM.

       squizz can do some conversions too, if the format the input format is supported. Only 3 types are available : sequence to sequence, align-
       ment to alignment, and alignment to sequence (the last one, sequence to alignment, require multiple alignments algorithms and cannot be
       handled with formatting tools).

       Strict format checks validate the previously detected objects, by making some sanity checks:

       - sequence strings must exists.
       - alignment is made of more than one sequence.
       - alignment sequence strings must have the same length.
       - alignment sequence names must exists, and be unique.

SEE ALSO

       seqfmt(5), alifmt(5)

AUTHOR

       Nicolas Joly (njoly@pasteur.fr), Institut Pasteur.

Unix								    2009-05-19								 SQUIZZ(1)

Linux and UNIX Man Pages

glam2format(1) [debian man page]

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