Definition of "seed" in sequence alignment I would like to know what is meant by "seed" for various sequence aligners. How is it important?
The seed is the subset of a read used in the first step of an alignment. Many aligners work by a seed-and-extend model, wherein they first find all regions matching the "seed" and then extend the alignment around that allowing mistmatches and indels until it either gives up (and therefore uses a different seed) or finds a sufficiently good alignment.