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Pairwise Alignment
2 November 6, 2000 Ron Shamir Based in part on a scribe of Eti Ezra and Guy Gelles November 13th, 1998 Ofira Grebenshuk and Alex Feldman
Pairwise Alignment
Problem Definition and Biological Motivation
Motivation
Similarity and Difference
Nomenclature
Simplest model: Edit Distance
Models for Alignment
Global Alignment
Tabular computation of optimal alignment
The Traceback
Global Alignment in linear space
The Algorithm:
Alignment Graph
Local Alignment
Motivation
Computing local alignment
End free-space alignment
Motivation
Gap Penalty
Motivation
Gap penalties types
Constant gap weight model
Affine gaps penalty
Other Gap Penalty Models
Longest Common Non Contiguous Subsequence
Polymerase Chain Reaction
Bibliography
About this document ...
Peer Itsik
2000-11-20
