Split-alignment of genomes finds orthologies more accurately

• DOI: 10.1186/s13059-015-0670-9
• Publication Date: 2015-05-20T10:22:47Z
• Authors: Martin C Frith; Risa Kawaguchi
• Keywords: Similarity (geometry); Human genetics

We present a new pair-wise genome alignment method, based on simple concept of finding an optimal set local alignments. It gains accuracy by not masking repeats, and using statistical model to quantify the (un)ambiguity each part. Compared previous animal alignments, it aligns thousands locations differently with much higher similarity, strongly suggesting that alignments are non-orthologous. The methods suffer from overly-strong assumption long un-rearranged blocks. should help find interesting unusual features, such as fast-evolving elements micro-rearrangements, which confounded errors.