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last-align

genome-scale comparison of biological sequences

Variants:
LAST is software for comparing and aligning sequences, typically DNA or protein sequences. LAST is similar to BLAST, but it copes better with very large amounts of sequence data. Here are two things LAST is good at:

* Comparing large (e.g. mammalian) genomes. * Mapping lots of sequence tags onto a genome.

The main technical innovation is that LAST finds initial matches based on their multiplicity, instead of using a fixed size (e.g. BLAST uses 11-mers). This allows to map tags to genomes without repeat-masking, without becoming overwhelmed by repetitive hits. To find these variable-sized matches, it uses a suffix array (inspired by Vmatch). To achieve high sensitivity, it uses a discontiguous suffix array, analogous to spaced seeds.

Homepage:
Package version:128-1
Architecture:i386
Distribution:Debian
Filename:last-align_128-1_i386.deb

/usr/share/doc/last-align/NEWS.Debian.gz

last-align (39-1) unstable; urgency=low

  Old lastdb protein databases built with last-align version lower than 39
  won't work properly: you need to re-run lastdb.

 -- Charles Plessy <plessy@debian.org>  Mon, 02 Feb 2009 12:42:26 +0900


/usr/share/doc/last-align/FAQ.txt

Q: Does it matter which way round you do the alignment: e.g. cat
versus mouse, or mouse versus cat?

A: The results may be different.  When comparing two similar-sized
genomes, the difference should be minor.  When mapping tags to a
genome, you probably want the genome to be the database, and the tags
to be the query.  That way, for each tag, it will search for several
most-similar locations in th
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/usr/share/man/man1/last-dotplot.1.gz

LAST-DOTPLOT.PY(1)          User Commands         LAST-DOTPLOT.PY(1)



NAME
       last-dotplot.py  -  make  a  dotplot,  a.k.a. Oxford Grid, of
       alignments in LAST tabular format

DESCRIPTION
   Usage:
              last-dotplot.py   --help   last-dotplot.py   [options]
              last-tabular-output     dotplot.png    last-dotplot.py
              [options] last-tabular-output dotplot.
more»

/usr/share/man/man1/last-map-probs.1.gz

LAST-MAP-PROBS.PY(1)        User Commands       LAST-MAP-PROBS.PY(1)



NAME
       last-map-probs.p
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/usr/share/man/man1/last-reduce-alignments.1.gz

LAST-REDUCE-ALIGNMENTS.SH(1)User CommandLAST-REDUCE-ALIGNMENTS.SH(1)



NAME
       last-reduce-alig
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/usr/share/man/man1/last-remove-dominated.1.gz

LAST-REMOVE-DOMINATED.PY(1) User CommandsLAST-REMOVE-DOMINATED.PY(1)



NAME
       last-remove-domi
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/usr/share/man/man1/lastal.1.gz

LASTAL(1)                   User Commands                  LASTAL(1)



NAME
       lastal - genome-
more»

/usr/share/man/man1/lastdb.1.gz

LASTDB(1)                   User Commands                  LASTDB(1)



NAME
       lastdb - genome-
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