The art of sequence alignment

Abstract

Sequence similarity: why are we interested in, how do you define it Scoring metrics: what is important in similarity Scoring with DNA: integrating biological knowledge Scoring with proteins: integrating biological knowledge PAMs and BLOSUMs: the marriage of statistics and biology Gaps: how strong do they count? Constant, affine and concave gap penalties The dynamic programmig trick Global versus local Heuristics to get some speed Can we trust our alignment? PSI-BLAST & Co: highlights and traps Multiple Sequence Alignment: finding and scoring them The third dimension From alignments to trees Beyond alignments