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since 2008

LAST finds similar regions between sequences.

sketch of
similar regions in sequences

LAST can:


What distinguishes LAST from BLAST and similar tools (e.g. BLAT, LASTZ, YASS)?

What distinguishes LAST from DNA read mapping tools?

Here are some dotplots made using LAST:


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).

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