title: Measuring the accuracy of genome-size multiple alignments.
abstract: Whole-genome alignments are invaluable for comparative genomics. Before doing any comparative analysis on a region of interest, one must have confidence in that region's alignment. We provide a methodology to measure the accuracy of arbitrary regions of these alignments, and apply it to the UCSC Genome Browser's 17-vertebrate alignment. We identify 9.7% (21 Mbp) of the human chromosome 1 alignment as suspiciously aligned. We present independent evidence that many of these suspicious regions represent misalignments.
authors.affiliation: Department of Computer Science and Engineering, University of Washington, Seattle, WA 98195-2350, USA. amol.prakash@thermofisher.com
authors.forename: Amol
authors.initials: A
authors.lastname: Prakash
authors.forename: Martin
authors.initials: M
authors.lastname: Tompa
mesh_terms: D000465:Algorithms; D000818:Animals; D001483:Base Sequence; D002878:Chromosomes, Human, Pair 1; D016678:Genome; D006801:Humans; D016415:Sequence Alignment / Q000379:methods*; D012689:Sequence Homology, Nucleic Acid; D012984:Software