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Measuring the accuracy of genome-size multiple alignments

Amol Prakash12* and Martin Tompa13

Author Affiliations

1 Department of Computer Science and Engineering, University of Washington, Seattle, WA 98195-2350, USA

2 Thermo BRIMS Center, Memorial Drive, Cambridge, MA 02139, USA

3 Department of Genome Sciences, University of Washington, Seattle, WA 98195-2350, USA

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Genome Biology 2007, 8:R124  doi:10.1186/gb-2007-8-6-r124

Published: 26 June 2007


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.