Abstract
This chapter compares global and local alignment, discusses the alignment tools that combine both local and global procedures into single algorithms, and examines dynamic programming and its application to pairwise global and local sequence alignment. ProbCons, a recent development in global multiple alignment, uses pair hidden Markov models to calculate optimal alignments based on a probabilistic sequence model. MatchBox is used to search for several local multiple alignments in a given input data set. The program DIALIGN has been designed as a combination of local and global alignment approaches, and constructs pairwise or multiple alignments by using gap-free local pairwise alignments as elementary alignments that are used to assemble a resulting pairwise or multiple alignment. The chapter ends with a discussion of the challenges and tools developed for full genome alignment.
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