Parallel homologous sequence searching in large databases

Author

Yap, Tieng K. ; Frieder, Ophir ; Martino, Robert L.

Author_Institution

Div. of Comput. Res. & Technol., Nat. Inst. of Health, Bethesda, MD, USA

fYear

1995

fDate

6-9 Feb 1995

Firstpage

231

Lastpage

237

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

Keywords

biology computing; dynamic programming; parallel programming; very large databases; dynamic programming; dynamic programming comparison; genetic databases; homologous sequence searching; large databases; parallel computational method; performance; protein databases; Biology computing; Computer aided instruction; Concurrent computing; Contracts; Databases; Dynamic programming; Genetics; Heuristic algorithms; Information retrieval; Proteins;

fLanguage

English

Publisher

ieee

Conference_Titel

Frontiers of Massively Parallel Computation, 1995. Proceedings. Frontiers '95., Fifth Symposium on the

Conference_Location

McLean, VA

Print_ISBN

0-8186-6965-9

Type

conf

DOI

10.1109/FMPC.1995.380444

Filename

380444