PerFSeeB: designing long high-weight single spaced seeds for full sensitivity alignment with a given number of mismatches.

ABSTRACT:

Background

Technical progress in computational hardware allows researchers to use new approaches for sequence alignment problems. For a given sequence, we usually use smaller subsequences (anchors) to find possible candidate positions within a reference sequence. We may create pairs ("position", "subsequence") for the reference sequence and keep all such records without compression, even on a budget computer. As sequences for new and reference genomes differ, the goal is to find anchors, so we tolerate differences and keep the number of candidate positions with the same anchors to a minimum. Spaced seeds (masks ignoring symbols at specific locations) are a way to approach the task. An ideal (full sensitivity) spaced seed should enable us to find all such positions subject to a give

SUBMITTER: Titarenko V 

PROVIDER: S-EPMC10594774 | biostudies-literature | 2023 Oct

REPOSITORIES: biostudies-literature