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glam2-purge(1) [debian man page]

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

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 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 <> 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)

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BLASTCLUST(1)						     NCBI Tools User's Manual						     BLASTCLUST(1)

blastclust - BLAST score-based single-linkage clustering SYNOPSIS
blastclust [-] [-C] [-L X] [-S X] [-W N] [-a N] [-b F] [-c filename] [-d filename] [-e F] [-i filename] [-l filename] [-o filename] [-p F] [-r filename] [-s filename] [-v [filename]] DESCRIPTION
blastclust automatically and systematically clusters protein or DNA sequences based on pairwise matches found using the BLAST algorithm in case of proteins or Mega BLAST algorithm for DNA. In the latter case a single Mega BLAST search is performed for all the sequences combined against a database created from the same sequences. blastclust finds pairs of sequences that have statistically significant matches and clusters them using single-linkage clustering. OPTIONS
A summary of options is included below. - Print usage message -C Complete unfinished clustering -L X Length coverage threshold (default = 0.9) -S X Score coverage threshold (bit score / length if < 3.0, percentage of identities otherwise; default = 1.75) -W N Use words of size N (length of best perfect match; zero invokes default behavior: 3 for proteins, 32 for nucleotides) -a N Number of CPU's to use (default = 1) -b F Do not require coverage on both neighbours -c filename Read advanced options from configuration file filename -d filename Input as a database -e F Disable id parsing in database formatting -i filename FASTA input file (program will format the database and remove files in the end; default = stdin) -l filename Restrict reclustering to id list in filename -o filename Output file for list of clusters (default = stdout) -p F Input is nucleotides, not proteins. -r filename Restore neighbors for reclustering from filename -s filename Save all neighbours to filename -v [filename] Print verbose progress messages (to filename) AUTHOR
The National Center for Biotechnology Information. SEE ALSO
blast(1), formatdb(1), /usr/share/doc/blast2/blastclust.html, <> NCBI
2004-06-25 BLASTCLUST(1)
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