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glam2-purge(1) [debian man page]

GLAM2-PURGE(1)							   glam2 Manual 						    GLAM2-PURGE(1)

NAME

       glam2-purge - Removes redundant sequences from a FASTA file

SYNOPSIS

       glam2-purge file score [options]

DESCRIPTION

       glam2-purge is a modified version of Andrew Neuwald's purge program that removes redundant sequences from a FASTA file. This is recommended
       in order to prevent highly similar sequences distorting the search for motifs. Purge works with either DNA or protein sequences and creates
       an output file such that no two sequences have a (gapless) local alignment score greater than a threshold specified by the user. The output
       file is named <file>.<score>. The alignment score is based on the BLOSUM62 matrix for proteins, and on a +5/-1 scoring scheme for DNA.
       Purge can also be used to mask tandem repeats. It uses the XNU program for this purpose.

OPTIONS

       -n
	   Sequences are DNA (default: protein).

       -b
	   Use blast heuristic method (default for protein).

       -e
	   Use an exhaustive method (default for DNA).

       -q
	   Keep first sequence in the set.

       -x
	   Use xnu to mask protein tandem repeats.

SEE ALSO

       glam2(1), glam2format(1), glam2mask(1), glam2scan(1), xnu(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/.

REFERENCES

       Purge was written by Andy Neuwald and is described in more detail in Neuwald et al., "Gibbs motif sampling: detection of bacterial outer
       membrane protein repeats", Protein Science, 4:1618-1632, 1995. Please cite it if you use Purge.

       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

       Andrew Neuwald
	   Author of purge, renamed glam2-purge in Debian.

       Martin Frith
	   Modified purge to be ANSI standard C and improved the user interface.

       Timothy Bailey
	   Modified purge to be ANSI standard C and improved the user interface.

       Charles Plessy <plessy@debian.org>
	   Formatted this manpage in DocBook XML for the Debian distribution.

COPYRIGHT

       The source code and the documentation of Purge and GLAM2 are released in the public domain.

GLAM2 1056							    05/19/2008							    GLAM2-PURGE(1)

Check Out this Related Man Page

THESEUS_ALIGN(1)					      General Commands Manual						  THESEUS_ALIGN(1)

NAME

       theseus_align - quick-and-dirty way to superimpose proteins

SYNOPSIS

       theseus_align [theseus options] -f pdbfile1.pdb pdbfile2.pdb ...

OPTIONS

       The options given to the script will be passed on to theseus. For a complete description, see the man page for theseus (1).

DESCRIPTION

       This  manual  page briefly documents briefly the script theseus_align, designed for a quick-and-dirty way to ML superposition proteins with
       different sequences. It should work very well when the protein sequences are relatively similar, although the ML  method  will  still  give
       much  better  results  than least-squares when the sequences are moderately divergent.  Technically, this procedure gives a structure-based
       superposition of a sequence-based alignment. It does not perform a structure-based alignment.

       First, the script uses theseus to create FASTA formatted sequence files corresponding to the exact protein sequences found in the pdb files
       that you supply.

       Second,	these  sequences  are  aligned using the multiple sequence alignment program of your choice. The script can easily be modified for
       CLUSTALW, T_COFFEE, KALIGN, DIALIGN2, or MAFFT. Any multiple sequence alignment program can be used, as long as it  can	generate  clustal-
       formatted  files.  However,  I  highly  recommend  Bob  Edgar's	MUSCLE	program  for  both  its  speed	and  accuracy.	(For more info see
       http://www.drive5.com/muscle/ .)

       Third, theseus performs a superposition of the structures using the sequence alignment as a guide.

       The installed version of theseus_align uses muscle (1) for doing the multiple sequence alignment. If you wish to use one of the other  pro-
       grams mentioned above, you'll have to copy the script to your own directory and edit it.

SEE ALSO

       theseus (1), muscle (1), clustalw (1), t_coffee (1), kalign (1), dialign2 (1), mafft (1).  All of these programs can be installed on Debian
       or Ubuntu systems using apt-get (8).

AUTHOR

       theseus_align was written by Douglas L. Theobald, Department of Biochemistry, Brandeis University.

								  November, 2008						  THESEUS_ALIGN(1)
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