Comparing Genome-Size Multiple Alignments

In the June 2010 issue of Nature Biotechnology, Xiaoyu Chen and Martin Tompa assessed four expert ENCODE alignments, each of which aligns 28 vertebrate sequences on 554,000,000 base-pairs of total input sequence. They reported a disturbing lack of agreement among the alignments not only in species distant from human, but even in mouse, a well-studied model organism. Overall, the assessment showed that the Pecan alignment method produced the most accurate or nearly most accurate alignment in all species and genomic location categories, while still providing coverage comparable to or better than that of the other alignments.

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Martin Tompa