Jali (Jumping Alignments) is an alignment method for comparing a protein sequence to a protein family, represented by a multiple alignment. It can also be used for sensitive protein database searches. The algorithm is a generalization of the Smith-Watherman algorithm.
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A novel approach to remote homology detection: Jumping Alignments
R. Spang, M. Rehmsmeier, J. Stoye
J. Comp. Biol., volume 9, pp. 747-760, 2002