FMAlign2: a novel fast multiple nucleotide sequence alignment method for ultralong datasets.

ABSTRACT:

Motivation

In bioinformatics, multiple sequence alignment (MSA) is a crucial task. However, conventional methods often struggle with aligning ultralong sequences. To address this issue, researchers have designed MSA methods rooted in a vertical division strategy, which segments sequence data for parallel alignment. A prime example of this approach is FMAlign, which utilizes the FM-index to extract common seeds and segment the sequences accordingly.

Results

FMAlign2 leverages the suffix array to identify maximal exact matches, redefining the approach of FMAlign from searching for global chains to partial chains. By using a vertical division strategy, large-scale problem is deconstructed into manageable tasks, enabling parallel execution of subMSA. Furthermore, sequence-profil

SUBMITTER: Zhang P 

PROVIDER: S-EPMC10809904 | biostudies-literature | 2024 Jan

REPOSITORIES: biostudies-literature