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* 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.
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 <firstname.lastname@example.org> Mon, 02 Feb 2009 12:42:26 +0900
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 more»
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»
LAST-MAP-PROBS.PY(1) User Commands LAST-MAP-PROBS.PY(1) NAME last-map-probs.p more»
LAST-REDUCE-ALIGNMENTS.SH(1)User CommandLAST-REDUCE-ALIGNMENTS.SH(1) NAME last-reduce-alig more»
LAST-REMOVE-DOMINATED.PY(1) User CommandsLAST-REMOVE-DOMINATED.PY(1) NAME last-remove-domi more»
LASTAL(1) User Commands LASTAL(1) NAME lastal - genome- more»
LASTDB(1) User Commands LASTDB(1) NAME lastdb - genome- more»