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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 10-mers). This allows one 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:199-1
Architecture:kfreebsd-amd64
Distribution:Debian
Filename:last-align_199-1_kfreebsd-amd64.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: Is there a multi-core / multi-threaded version of LAST?

A: No, but you can easily do it yourself.  Suppose you want to compare
   sequences in three files (dna1.fa, dna2.fa, dna3.fa) to a lastdb
   database called "mydb".  You can do something like this:

     lastal mydb dna1.fa > out1.maf &
     lastal mydb dna2.fa > out2.maf &
     lastal mydb dna3.fa > out3.maf &

  This will process the f
more»

/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-merge-batches.1.gz

LAST-MERGE-BATCHES.PY(1)    User Commands   LAST-MERGE-BATCHES.PY(1)



NAME
       last-merge-batch
more»

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

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



NAME
       last-pair-probs.
more»

/usr/share/man/man1/last-reduce-alignments.1.gz

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



NAME
       last-reduce-alig
more»

/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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