生物信息学两两序列比对.ppt

PAM matrices are based on global alignments of closely related proteins. The PAM1 is the matrix calculated from comparisons of sequences with no more than 1% divergence. At an evolutionary interval of PAM1, one change has occurred over a length of 100 amino acids. Other PAM matrices are extrapolated from PAM1. For PAM250, 250 changes have occurred for two proteins over a length of 100 amino acids. All the PAM data come from closely related proteins (85% amino acid identity). PAM matrices: Point-accepted mutations Page 63 Dayhoff’s PAM1 mutation probability matrix Page 66 Dayhoff’s PAM0 mutation probability matrix: the rules for extremely slowly evolving proteins Top: original amino acid Side: replacement amino acid Page 68 Dayhoff’s PAM2000 mutation probability matrix: the rules for very distantly related proteins PAM? A Ala R Arg N Asn D Asp C Cys Q Gln E Glu G Gly A 8.7% 8.7% 8.7% 8.7% 8.7% 8.7% 8.7% 8.7% R 4.1% 4.1% 4.1% 4.1% 4.1% 4.1% 4.1% 4.1% N 4.0% 4.0% 4.0% 4.0% 4.0% 4.0% 4.0% 4.0% D 4.7% 4.7% 4.7% 4.7% 4.7% 4.7% 4.7% 4.7% C 3.3% 3.3% 3.3% 3.3% 3.3% 3.3% 3.3% 3.3% Q 3.8% 3.8% 3.8% 3.8% 3.8% 3.8% 3.8% 3.8% E 5.0% 5.0% 5.0% 5.0% 5.0% 5.0% 5.0% 5.0% G 8.9% 8.9% 8.9% 8.9% 8.9% 8.9% 8.9% 8.9% Top: original amino acid Side: replacement amino acid Page 68 PAM250 mutation probability matrix Top: original amino acid Side: replacement amino acid Page 68 PAM250 log odds scoring matrix Page 69 Why do we go from a mutation probability matrix to a log odds matrix? We want a scoring matrix so that when we do a pairwise alignment (or a BLAST search) we know what score to assign to two aligned amino acid residues. Logarithms are easier to use for a scoring system. They allow us to sum the scores of aligned residues (rather than having to multiply them). Page 69 How do we go from a mutation probability matrix to a log odds matrix? The cells in a log odds matrix consist of an “odds ratio”: the probability that an alignment is authentic the probability t