Expand description
BLAST-style seed-and-extend local alignment.
Classic heuristic local aligner: index every exact k-mer (“seed”) shared
between the query and the subject, then extend each seed in both directions
with an ungapped X-drop extension to grow high-scoring segment pairs
(HSPs). This trades the optimality of Smith–Waterman for near-linear speed
on long sequences, finding only the alignments anchored by an exact seed.
Structs§
- Blast
Aligner - Seed-and-extend aligner with a validated configuration.
- Blast
Config - Configuration for the seed-and-extend aligner.
- Hsp
- A high-scoring segment pair (ungapped local alignment) found by extension.