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Local versus global alignment

The Kruskal and Sankoff version of the local alignment is implemented [#!SanKru83!#]; this is very similar to the [#!SmiWat81!#] method. All the routines for the local alignment are exactly the same as the routines for the global alignment except that during the construction of matrix $D$ the alignment is restarted each time the score becomes higher than a cutoff. The second difference is that the backtracking starts from the lowest element in the matrix, wherever it is.



Bozidar BJ Jerkovic 2001-12-21