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Genome Biology

, 8:R124

First Online: 26 June 2007Received: 05 September 2006Revised: 07 December 2006Accepted: 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.

Electronic supplementary materialThe online version of this article doi:10.1186-gb-2007-8-6-r124 contains supplementary material, which is available to authorized users.

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Autor: Amol Prakash - Martin Tompa


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