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Sequence Alignments In Bioinformatics Lecture by: Ms AQSAD RASHDAPowerPoint Presentation

Sequence Alignments In Bioinformatics Lecture by: Ms AQSAD RASHDA

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### Sequence Alignments In BioinformaticsLecture by: Ms AQSAD RASHDA

THE EVOLUTIONARY BASIS OF SEQUENCE ALIGNMENT

Similarity

Homology

The changes: Substitutions, insertions, and deletions.

Gaps

Pairwise alignmentDot-matrix

OPTIMAL ALIGNMENT METHODS

Dynamic programming

Needleman-Wunsch algorithm

Smith-Waterman algorithm

SIM algorithm: A program called lalign

SUBSTITUTION SCORES AND GAP PENALTIES

Substitution matrix for proteins

Isoleucine for valine

Serine for threonine

Alignment scores

Point accepted mutation (PAM) model of evolution

Background frequencies

Substitution frequencies (target frequencies) in related proteins

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