Documentation : https://gitlab.com/mcfrith/last

LAST finds similar regions between sequences.

The main technical innovation is that LAST finds initial matches based on their multiplicity, instead of using a fixed length (e.g. BLAST uses 11-mers). To find these variable-length matches, it uses a suffix array (inspired by Vmatch). To achieve high sensitivity, it uses a spaced suffix array (or subset suffix array), analogous to spaced seeds (or subset seeds).

LAST can:

• Handle big sequence data, e.g:

  • Compare two vertebrate genomes.
  • Align billions of DNA reads to a genome.

• Indicate the reliability of each aligned column.
• Use sequence quality data properly.
• Compare DNA to proteins, with frameshifts.
• Compare PSSMs to sequences.
• Calculate the likelihood of chance similarities between random sequences.
• Do split and spliced alignment.
• Train alignment parameters for unusual kinds of sequence (e.g. nanopore).