Parallel homologous sequence searching in large databases

Authors:
T. K. Yap;O. Frieder;R. L. Martino
Affiliations:
-;-;-
Venue:
FRONTIERS '95 Proceedings of the Fifth Symposium on the Frontiers of Massively Parallel Computation (Frontiers'95)
Year:
1995

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Abstract

We present a parallel computational method for retrieving similar sequences from large genetic and protein databases using a dynamic programming comparison algorithm. Two previously published parallel methods for performing this task are first discussed and evaluated. The advantages of these two parallel methods are combined and incorporated into our new method to obtain better performance than either of the original two. Using the entire GenBank database (release 80.0), we compare the performance of the three methods on an Intel iPSC/860 parallel computer.