03-511/711, 15-495/856 Course Notes - August 31, 2010

Pairwise alignment continued

Alignment algorithms

The dynamic programs for sequence alignment compute a matrix a[i,j], which gives the scores of the optimal alignments of all prefixes. These algorithms have four components:

The details of each of these steps are what differentiate global, semi-global and local alignment.

Global alignment with similarity scoring

In this case, all matches are accorded the same weight, as are all mismatches. Later in the semester we will consider substitution matrices where the scores for matches and mismatches vary for different characters i and j.

Under this simple scoring function, the dynamic programming algorithm for global alignment has the following initialization and recursion steps:

Semiglobal Alignment

Semiglobal alignment is global alignment with no end gap penalties. Some applications include:

The global dynamic programming algorithm can be modified for semi-global alignment as follows:

Last modified: August 31, 2010.
Maintained by Dannie Durand (durand@cs.cmu.edu) and Annette McLeod.