Lookup table

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In genomics, a lookup table is a tool to quickly find specific kmers, usually 12-mers, within a known reference sequence. Lookup tables are created by pre-processing the reference sequence, and are used by "looking up" query sequences within the table.

Lookup tables are commonly used to find alignments where one of the sequences is very large, such as a reference genome, and can therefore be pre-processed. For example, the BLAST program uses a pre-processed lookup table to align query sequences to known genomes.

In Arachne, lookup tables are stored in Arachne binary format in files with the lookup extension, i.e., genome.lookup.

Modules that handle lookup tables include:

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