Genome Biology
Volume 8
Issue 6 |
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 MethodMeasuring the accuracy of genome-size multiple alignmentsAmol Prakash1,2  and Martin Tompa1,3  1Department of Computer Science and Engineering, University of Washington, Seattle, WA 98195-2350, USA 2Thermo BRIMS Center, Memorial Drive, Cambridge, MA 02139, USA 3Department of Genome Sciences, University of Washington, Seattle, WA 98195-2350, USA  author email corresponding author email
Genome Biology 2007,
8:R124doi:10.1186/gb-2007-8-6-r124
Subject areas: Genome studies, Bioinformatics 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. | 
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