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LAST
since 2008

LAST finds similar regions between sequences.

sketch of
similar regions in sequences

LAST can:

Documents:

Development & old versions:

Here are some dotplots made using LAST:

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

What distinguishes LAST from DNA read mapping tools?

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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