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Split-alignment of genomes finds orthologies more accurately

Author:
Frith, Martin C, Kawaguchi, Risa
Source:
GenomeBiology.com 2015 v.16 no.1 pp. 106
ISSN:
1465-6906
Subject:
animals, genome, statistical models
Abstract:
We present a new pair-wise genome alignment method, based on a simple concept of finding an optimal set of local alignments. It gains accuracy by not masking repeats, and by using a statistical model to quantify the (un)ambiguity of each alignment part. Compared to previous animal genome alignments, it aligns thousands of locations differently and with much higher similarity, strongly suggesting that the previous alignments are non-orthologous. The previous methods suffer from an overly-strong assumption of long un-rearranged blocks. The new alignments should help find interesting and unusual features, such as fast-evolving elements and micro-rearrangements, which are confounded by alignment errors.
Agid:
1522755