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LAST finds similar regions between sequences.

What distinguishes LAST from BLAST and similar tools (e.g. BLAT, LASTZ, YASS)? The main difference is that it copes more efficiently with repeat-rich sequences (e.g. genomes). For example, it can align reads to genomes without repeat-masking and without becoming overwhelmed by repetitive hits.

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.

LAST cannot (yet):

  • Do spliced alignment

Required Modules

modules documentation


  • last

System Variables

  • HPC_{{#uppercase:last}}_DIR - installation directory


  • Validated 4/5/2018