Accurate multiple alignment of distantly related genome sequences using filtered spaced word matches as anchor points.

ABSTRACT:

Motivation

Most methods for pairwise and multiple genome alignment use fast local homology search tools to identify anchor points, i.e. high-scoring local alignments of the input sequences. Sequence segments between those anchor points are then aligned with slower, more sensitive methods. Finding suitable anchor points is therefore crucial for genome sequence comparison; speed and sensitivity of genome alignment depend on the underlying anchoring methods.

Results

In this article, we use filtered spaced word matches to generate anchor points for genome alignment. For a given binary pattern representing match and don't-care positions, we first search for spaced-word matches, i.e. ungapped local pairwise alignments with matching nucleotides at the match positions of the pattern

SUBMITTER: Leimeister CA 

PROVIDER: S-EPMC6330006 | biostudies-literature | 2019 Jan

REPOSITORIES: biostudies-literature