glam2(1) [debian man page]

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)

Check Out this Related Man Page

BP_REVTRANS-MOTIF(1p)					User Contributed Perl Documentation				     BP_REVTRANS-MOTIF(1p)

NAME

       revtrans-motif - Reverse translate a Profam-like protein motif

VERSION

       Version 0.01

SYNOPSIS

       From a file:

	   revtrans-motif.pl -i motifs.txt

       Using pipes:

	  revtrans-motif.pl < motifs.txt > output.txt

       Using interactively at the command prompt:

	  $ revtrans-motif.pl
	  MAAEEL[VIKP]
	  1.   ATGGCNGCNGARGARYTNVHN
	  [^P]H(IW){2,3}
	  2.   NDNCAY(ATHTGG){2,3}

DESCRIPTION

       This script takes a protein motif as input and returns a degenerate oligonucleotide sequence corresponding to it. The main reason for doing
       this is to design degenerate primers that amplify a given sequence pattern.

       The input motif consists of a string of one-letter residues, with any of the following syntactic elements:

       [...] : Redundant position.
	   A position in which more than one residue is allowed. Example:

	       [TS]YW[RKSD]
		^^    ^^^^

       [^...] : Negated position.
	   A position in which any residue is allowed, saved for those between brackets. Example:

	       [^PW]MK[LAE]
		 ^^

       (...){n,m,...} : Repeated motif.
	   A motif that is repeated n or m times. It can have any of the previous syntactic elements. Example:

	       A[SN]C(TXX){2,4,8}
		      ^^^

       The allowed letters are those that correspond to the 20 natural aminoacids, plus:

	   B = N + D
	   Z = Q + E
	   X = All

OPTIONS

   -i input-file:
       A file with a list of motifs to reverse translate.

   -h
       Display this help message.

AUTHOR

       Bruno Vecchi, "vecchi.b at gmail.com"

BUGS

       Please report any bugs or feature requests to "vecchi.b at gmail.com"

COPYRIGHT &; LICENSE
       Copyright 2009 Bruno Vecchi, all rights reserved.

       This program is free software; you can redistribute it and/or modify it under the same terms as Perl itself.

perl v5.14.2							    2012-03-02						     BP_REVTRANS-MOTIF(1p)

Linux and UNIX Man Pages

glam2(1) [debian man page]

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