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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

DOTTER:(1)						      General Commands Manual							DOTTER:(1)

NAME

       dotter - Sequence dotplots with image enhancement tools.

SYNOPSIS

       dotter [options] <horizontal_sequence> <vertical_sequence> [X options]

DESCRIPTION

	      Reference:  Sonnhammer ELL & Durbin R (1995). A dot-matrix program with dynamic threshold control suited for genomic DNA and protein
	      sequence analysis. Gene 167(2):GC1-10.

       Allowed types:
	      Protein	     -	    Protein DNA 	   -	  DNA DNA	     -	    Protein

	      Options:

       -b <file>
	      Batch mode, write dotplot to <file>

       -l <file>
	      Load dotplot from <file>

       -m <float>
	      Memory usage limit in Mb (default 0.5)

       -z <int>
	      Set zoom (compression) factor

       -p <int>
	      Set pixel factor manually (ratio pixelvalue/score)

       -W <int>
	      Set sliding window size. (K => Karlin/Altschul estimate)

       -M <file>
	      Read in score matrix from <file> (Blast format; Default: Blosum62).

       -F <file>
	      Read in sequences and data from <file> (replaces sequencefiles).

       -f <file>
	      Read feature segments from <file>

       -H     Do not calculate dotplot at startup.

       -R     Reversed Greyramp tool at start.

       -r     Reverse and complement horizontal_sequence (DNA vs Protein)

       -D     Don't display mirror image in self comparisons

       -w     For DNA: horizontal_sequence top strand only (Watson)

       -c     For DNA: horizontal_sequence bottom strand only (Crick)

       -q <int>
	      Horizontal_sequence offset

       -s <int>
	      Vertical_sequence offset

	      Some X options: -acefont <font> Main font.  -font    <font> Menu font.

SEE ALSO

       http://www.cgb.ki.se/cgb/groups/sonnhammer/Dotter.html for more info.

AUTHOR

       Erik.Sonnhammer@cgb.ki.se Version 3.1, compiled Jul 10 2010

								     July 2010								DOTTER:(1)
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