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lastal(1) [debian man page]

LASTAL(1)							   User Commands							 LASTAL(1)

NAME

       lastal - genome-scale comparison of biological sequences

SYNOPSIS

       lastal [options] lastdb-name fasta-sequence-file(s)

DESCRIPTION

       Find local sequence alignments.

       Score  options  (default  settings): -r: match score   (DNA: 1, protein: blosum62, 0<Q<5:  6) -q: mismatch cost (DNA: 1, protein: blosum62,
       0<Q<5: 18) -p: file for residue pair scores -a: gap existence cost (DNA: 7, protein: 11, 0<Q<5: 21) -b: gap extension cost  (DNA:  1,  pro-
       tein:   2,  0<Q<5:   9)	-c:  unaligned	residue  pair cost (100000) -F: frameshift cost (off) -x: maximum score drop for gapped alignments
       (max[y, a+b*20]) -y: maximum score drop for gapless alignments (t*10) -z: maximum score drop for final gapped alignments  (x)  -d:  minimum
       score for gapless alignments (e*3/5) -e: minimum score for gapped alignments (DNA: 40, protein: 100, 0<Q<5: 180)

       Cosmetic  options  (default  settings): -h: show all options and their default settings -v: be verbose: write messages about what lastal is
       doing -o: output file -f: output format: 0=tabular, 1=maf (1)

       Miscellaneous options (default settings): -s: strand: 0=reverse, 1=forward, 2=both (2 for DNA, 1 for protein) -m: maximum multiplicity  for
       initial	matches (10) -l: minimum length for initial matches (1) -n: maximum number of gapless alignments per query position (infinity) -k:
       step-size along the query sequence (1) -i: query batch size (1 MiB if Q>0, else 16 MiB if j=0, else 128	MiB)  -u:  mask  lowercase  during
       extensions: 0=never, 1=gapless,

	      2=gapless+gapped but not final, 3=always (2 if lastdb -c and Q<5, else 0)

       -w:  supress  repeats  inside exact matches, offset by this distance or less (1000) -G: genetic code file -t: 'temperature' for calculating
       probabilities (1/lambda) -g: 'gamma' parameter for gamma-centroid and LAMA (1) -j: output  type:  0=match  counts,  1=gapless,  2=redundant
       gapped, 3=gapped,

	      4=column ambiguity estimates, 5=gamma-centroid, 6=LAMA (3)

       -Q: input format: 0=fasta, 1=fastq-sanger, 2=fastq-solexa, 3=fastq-illumina,

	      4=prb, 5=PSSM (0)

REPORTING BUGS

       Report bugs to: last (ATmark) cbrc (dot) jp
       LAST home page: http://last.cbrc.jp/

lastal 199							     May 2012								 LASTAL(1)

Check Out this Related 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)
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