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Genome Biol. 2007;8(6):R124.

Measuring the accuracy of genome-size multiple alignments.

Author information

  • 1Department of Computer Science and Engineering, University of Washington, Seattle, WA 98195-2350, USA. amol.prakash@thermofisher.com


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.

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