Transcription of Lecture 2 Pairwise sequence alignment.
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Lecture 2 Pairwise sequence alignment.
Lecture 2 Pairwise sequence alignment . Principles Computational Biology Teresa Przytycka, PhD Assumptions: Biological sequences evolved by evolution. Micro scale changes: For short sequences ( one domain proteins) we usually assume that evolution proceeds by: Substitutions Human MSLICSISNEVPEHPCVSPVS .. Insertions/Deletions Protist MSIICTISGQTPEEPVIS-KT .. Macro scale changes: For large sequences ( whole genomes) we additionally allow, Duplications reversals Protein segments known as domains are reused by different proteins (via various mechanisms) Importance of sequence comparison Discovering functional and evolutional relationships in biological sequences: Similar sequences ! evolutionary relationship evolutionary relationship ! related function Orthologs ! same (almost same) function in different organisms.
Dynamic programming algorithm for computing the score of the best alignment For a sequence S = a 1, a 2, …, a n let S j = a 1, a 2, …, a j S,S’ – two sequences Align(S i,S’ j) = the score of the highest scoring alignment between S1 i,S2 j S(a i, a’ j)= similarity score between amino acids a i and a j given by a scoring matrix like ...
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