Bioalgo 2013-08-alignment-3
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The document discusses different alignment techniques for sequences including affine gap penalties where the penalty for a gap of length l is equal to the gap open penalty plus the gap extend penalty multiplied by l minus 1. It provides an example where the Needleman-Wunsch algorithm produces a counterintuitive alignment and discusses multiple sequence alignment techniques like progressive alignments and iterative methods which are useful but computationally difficult problems.
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Bioalgo 2013-08-alignment-3
- 2. Affine gap penalty penalty = gap_open + gap_extend * (l-1), l -- length of the gap
- 3. Needleman-Wunsch counterexample open=-3, extend=-1, math=0, mismatch=-5 AT GC AT-- --GC - A T - 0 -3 -4 G -3 -5 -8 C -4 -8 -10
- 7. Multiple sequence alignment ● useful ● hard ● NP-hard ● dynamic programming =( ● progressive alignments ● iterative methods