Space and time optimal parallel sequence alignments

We present the first space and time optimal parallel algorithm for the pairwise sequence alignment problem, a fundamental problem in computational biology. This problem can be solved sequentially in O(mn) time and O(m+n) space, where m and n are the lengths of the sequences to be aligned. The fastes...

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Veröffentlicht in:	IEEE transactions on parallel and distributed systems 2004-12, Vol.15 (12), p.1070-1081
Hauptverfasser:	Rajko, S., Aluru, S.
Format:	Artikel
Sprache:	eng
Schlagworte:	Algorithms Alignment Biological system modeling Biology Clustering algorithms Clusters Computation Computational biology Concurrent computing Dynamic programming Economics Heuristic algorithms Optimization Parallel algorithms parallel dynamic programming Read-write memory Runtime sequence alignments Sequences space-efficient Studies Time optimal
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