Bioscan: A network sharable computational resource for searching biosequence databases

Bioinformatics

Volumn 12, Issue 3, 1996, Pages 191-196

  Singh, R K ^a   Hoffman, D L ^a   Tell, S G ^a   White, C J ^a  

^a Brooks Computer Science Building   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; COMPUTER; COMPUTER NETWORK; COMPUTER PROGRAM; DATA BASE; PRIORITY JOURNAL; PROTEIN ANALYSIS; SEQUENCE ANALYSIS;

ALGORITHMS; AMINO ACID SEQUENCE; BASE SEQUENCE; COMPUTER COMMUNICATION NETWORKS; DATABASES, FACTUAL; NUCLEIC ACIDS; PROTEINS; SEQUENCE ALIGNMENT; SOFTWARE;

EID: 0029958415     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/12.3.191     Document Type: Article

References (23)

1. Altschul.S.F (1991). Amino acid substitution matrices from an information theoretic perspective. J Mol. Bioi, 219, 555-565
2. Altschul.S.F., Gish.W., Miller.W., Myers.E.W. and Lipman.D.J. (1990) Basic local alignment search tool. J. Mol. Biol., 215, 403-410.
3. Bairoch, A. and Boeclcmann, B. (1994). The SWISS-PROT protein sequence data bank' current status. Nucleic Acids Res., 22, 3578-3580.
4. Barker.W, George.D., Mewes., H. and Tsugita.A (1992). Protein sequence database of the protein identification resource (PIR), National Biomedical Research Foundation, Georgetown University Medical Center. Nucleic Acids Res., 20, 2023-2026
5. Benson, D., Boguski.M., Lipman.D. and Ostell.J. (1994). Genbank. Nucleic Acids Res.. 22, 3441-3444
6. Brutlag.D., Dautrucourt.J., Fier.J., Moxon.B and Stamm.R. (1993). Blaze. Computational Chem., 17, 203
7. Chow, E.T., Hunkapiller, T., Peterson, J.C., Zimmerman, B.A. and Waterman, M.S. (1991). A systolic array processor for biological information signal processing. Proc. Int. Conference on Supercomputing, A. 216— 223
8. Compugen (1995). Bioccellerator User Guide. Compugen Ltd., Hama-cabim St. 17, Petah-Tikva, 49220 Israel.
9. DayhofT, M., Eck, R. and Park, C. (1972). A model of evolutionary change in proteins. In DayhofT, M. (ed.). Atlas of Protein Sequence and Structure, volume 5, pages 89-99.
10. DettlofT.W D., Singh.R.K., White, C.T. and Erickson, B.W. (1991). A 50 mhz 1.5m transistor ASIC for biosequence analysis. Int. Solid State Circuit Conference Digest of Technical Papers, pp. 40-42.
11. Gokhale.M., Holme.B., Kopser.A., Kunze.D., Lopresti, D., Lucas, S. and Olsen.P.R (1990). Splash: A reconfigurable linear logic array Proc. Int. Conference on Parallel Processing, pp. 526-532.
12. Henikoff.S. and HenikofU.G. (1992) Amino acid substitution matrices from protein blocks. Proc. Nat. Acad. of Sci. USA, 89, 10915-10919.
13. Hughey.R.P. and Lopresti.D.P. (1991). B-sys: A 470-processor programmable systolic array. Proc. Int. Conference on Parallel Processing, pp. 580-586
14. Karlin.S. and Altschul.S.F (1993) Application and statistics for multiple high-scoring segments in molecular sequences Proc. Natl. Acad. Sci USA, 90, 5873-5877
15. Lopresti.D. (1987). P-NAC: A systolic array for comparing nucleic acid sequences. Computer, 20, 98-99.
16. Needleman, S.B. and Wunsch.C.D. (1970). A general method applicable to the search for similarities in the amino acid sequence of two proteins. J. Mol. Biol., 48, 443-453.
17. Pearson.W.R. and Lipman.D.J. (1988). Improved tools for biological sequence comparison Proc Natl Acad. Sci. USA, 85, 2444-2448
18. Rigoutsos, I. and Califano, A. (1993). dFLASH: A distributed fast look-up algorithm for string homology. Technical report, IBM T. J Whatson Research Center, PO. Box 704, Yorktown Heights. NY 105698.
19. Singh, R K; Tell, S.G., White, C.T., Hoffman, D.L., Chi, V.L. and Enckson, B.W. (1993). A scalable systolic multiprocessor system for analysis of biological sequences. Proc. Symposium on Integrated Systems, pp. 167-182.
20. Smith.T.F. and Waterman, M.S. (1981). Comparison of biosequences. Adv. Appl. Math., 2, 482-489.
21. States.DJ., Gish.W and Altschul.S.F. (1991). Improved sensitivity of nucleic acid database searches using application-specific scoring matrices Methods Companion to Methods Enzymol, 3, 66-70
22. White, C.T., Singh, R.K., Reintjes, P.B., Lampe, l., Erickson, B.W., Dettloff, W.D., Chi, V.L. and Altschul, S.F. (1991). BioSCAN: A VLSI-based system for biosequence analysis. Proc Int. Conference on Computer Design. VLSI in Computers & Processors, pp. 504-509.
23. Wootton, J.C. and Federhen, S. (1993). Statistics of local complexity in amino acid sequences and sequence databases. Computers in Chemistry, 17, 149-163.