PowerPoint Slideshow about 'HEURISTIC APPROACHES' - mprasadnaidu

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FastA is an algorithm developed by Pearson and Lipman. Its more sensitive than Blast.

Blast is an algorithm developed by Altschul et al., in 1990. It provides tools for high scoring local alignment between two sequences. Now a days, a gapped versions are available.

Scoring schemes alignment starts after leaving three characters or residues

Identity scoring matrix

Residue to residue scores are represented here in the form of similarity.

A 4 X 4 matrix is built for the nucleotides and 20 X 20 matrix for the amino acids.

For match score is +1 and mismatch is -1

PAM Matrices alignment starts after leaving three characters or residues

These were first developed by Margaret Dayhoff and co-workers in 1978.

This model assumes that evolutionary changes follow the markov model i.e. residual changes occur independent on the previous mutation. One PAM is a unit of evolutionary divergence in which there is 1% amino acid change but it doesn’t imply that 100 PAM results in different aminoacids.

Dayhoff and coworkers have calculated the frequencies of accepted mutations for 1PAM by analyzing closely related families of sequences.

The scores are represented as log odd ratios.

The 1PAM can be extended to any no of PAMS. For example, 1PAM table is extended to N X 1PAM.

For closely related protein sequences, lower distance PAM is used and higher PAM is used for variying proteins.

PAM 30 is used for closer proteins and PAM 250 for divergent ones.