423f11-lec8-mummer

423f11-lec8-mummer - Alignment of Entire Genomes (MUMmer)...

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Unformatted text preview: Alignment of Entire Genomes (MUMmer) CMSC 423 Carl Kingsford Challenges aligning whole genomes genome A genome B regions of the genomes that align well (with some gaps & mismatches) rearrangements cant be represented in a standard MSA Aligning two sequences of 130 million letters isnt feasible using an O( n 2 ) algorithm. Dot Plots short region that is equal in both genomes green means the sequence in one genome matches the reverse complement of the sequence in the other s = ACCGGTG rc( s ) = CACCGGT A B 1 1 1 1 2 2 1 1 2 2 More Distant Organisms Shifts from the diagonal correspond to regions that have moved. Alignment Anchors x y a b Maximum Unique Match (MUM): a region that matches exactly between the two genomes, and exists exactly once in each genome, and is not contained in a longer such region The idea is that these unique, exact matches should almost always be aligned in the true alignment....
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This note was uploaded on 01/13/2012 for the course CMSC 423 taught by Professor Staff during the Fall '07 term at Maryland.

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423f11-lec8-mummer - Alignment of Entire Genomes (MUMmer)...

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