Anchor points for genome alignment based on Filtered Spaced Word Matches
Genomics
2017-03-28 v1
Abstract
Alignment of large genomic sequences is a fundamental task in computational genome analysis. Most methods for genomic alignment use high-scoring local alignments as {\em anchor points} to reduce the search space of the alignment procedure. Speed and quality of these methods therefore depend on the underlying anchor points. Herein, we propose to use {\em Filtered Spaced Word Matches} to calculate anchor points for genome alignment. To evaluate this approach, we used these anchor points in the the widely used alignment pipeline {\em Mugsy}. For distantly related sequence sets, we could substantially improve the quality of alignments produced by {\em Mugsy}.
Cite
@article{arxiv.1703.08792,
title = {Anchor points for genome alignment based on Filtered Spaced Word Matches},
author = {Chris-Andre Leimeister and Thomas Dencker and Burkhard Morgenstern},
journal= {arXiv preprint arXiv:1703.08792},
year = {2017}
}