Similar_Join: Extending DBMS with a bio-specific operator

Proceedings of the ACM Symposium on Applied Computing

Volumn , Issue , 2003, Pages 109-114

  Chen, Jake Yue ^a   Carlis, John V ^b  

^a Prolexys Pharmaceuticals Inc   (United States)

^b University of Minnesota   (United States)

Author keywords

Database Management System (DBMS); Genomic DBMS Extension; Relational Operator; Similar_Join Operator; Similarity Search

Indexed keywords

ALGORITHMS; AUTOMATION; COMPUTER PROGRAM LISTINGS; SYNTACTICS;

SIMILARITY SEARCH;

RELATIONAL DATABASE SYSTEMS;

EID: 0037661321     PISSN: None     EISSN: None     Source Type: Conference Proceeding    
DOI: None     Document Type: Conference Paper

References (32)

1. Altschul, S.F., et al., Basic local alignment search tool. J Mol Biol, 1990. 215(3): 403-10.
2. Altschul, S.F., et al., Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res, 1997. 25(17): 3389-402.
3. Boone, M. and C. Upton, BLAST Search Updater: a notification system for new database matches. Bioinformatics, 2000. 16(11): 1054-5.
4. Bucher, P. and K. Hofmann, A sequence similarity search algorithm based on a probabilistic interpretation of an alignment scoring system. Proc Int Conf Intell SystMol Biol, 1996. 4:44-51.
5. Carlis, J.V. HAS, a Relational Algebra Operator or Divide is not Enough to Conquer. in Second International Conference on Data Engineering. 1986. Los Angeles, California.
6. Carlis, J.V. and S. Krieger, Mastering Database Analysis. 2002, (to be published): Addison-Wesley.
7. Chen, J.Y., PhD Thesis; A Bioinformatics Discovery-oriented Framework, in Computer Science. 2001, University of Minnesota: Minneapolis, 185.
8. Chen, J.Y. and J.V. Carlis, Genomic Data Modeling. Information Systems, 2002. Special Issue on Bioinformatics and Biological Data Management.
9. Chi, E.H., et al. Visualization of Biological Sequence Similarity Search Results. in IEEE Visualization '95. 1995.
10. Durand, P., L. Canard, and J.P. Mornon, Visual BLAST and visual FASTA: graphic workbenches for interactive analysis of full BLAST and FASTA outputs under MICROSOFT WINDOWS 95/NT. Comput Appl Biosci, 1997, 13(4): 407-13.
11. Hannenhalli, S.S. and R.B. Russell, Analysis and prediction of functional sub-types from protein sequence alignments. J Mol Biol, 2000. 303(1): 61-76.
12. Held, J.P. and J.V. Carlis, MATCH - a new high-level relational operator for pattern matching. Communications of the ACM, 1987.30(1): 62-75.
13. Henikoff, S., S. Pietrokovski, and J.G. Henikoff, Superior performance in protein homology detection with the Blocks Database servers. Nucleic Acids Res, 1998. 26(1): 309-12.
14. Jenuth, J.P., The NCBI. Publicly available tools and resources on the Web. Methods Mol Biol, 2000. 132: 301-12.
15. Karp, P.D., A strategy for database interoperation. J Comput Biol, 1995. 2(4): 573-86.
16. Karplus, K., C. Barrett, and R. Hughey, Hidden Markov models for detecting remote protein homologies. Bioinformatics, 1998. 14(10): 846-56.
17. Kelley, L.A., R.M. MacCallum, and M.J. Sternberg, Enhanced genome annotation using structural profiles in the program 3D- PSSM. J Mol Biol, 2000. 299(2): 499-520.
18. Koretke, K.K., et al., Fold recognition using sequence and secondary structure information. Proteins, 1999. 37(S3): 141-148.
19. Krauthammer, M., et al., Using BLAST for identifying gene and protein names in journal articles. Gene, 2000. 259(1-2): 245-52.
20. Oracle, Oracle8i Server Application, Release 8.1.6. 1999, Oracle Corporation.
21. Pearson, W.R., Flexible sequence similarity searching with the FASTA3 program package. Methods Mol Biol, 2000. 132: 185-219.
22. Pearson, W.R. and D. J. Lipman, Improved tools for biological sequence comparison. Proc Natl Acad Sci USA, 1988. 85(8): 2444-8.
23. Schultz, J., et al., More than 1,000 putative new human signalling proteins revealed by EST data mining. Nat Genet, 2000. 25(2): 201-4.
24. Selley, J.N., J. Swift, and T.K. Attwood, EASY-an Expert Analysis SYstem for interpreting database search outputs. Bioinformatics, 2001. 17(1): 105-6.
25. Simakov, P., Sequence Server Samurai. Science, 1999. 285(5431): 1226-1227.
26. Smith, T.F. and M.S. Waterman, Identification of common molecular subsequences. Journal of Molecular Biology, 1981. 147(1): 195-7.
27. Smittipat, N. and P. Palittapongarnpim, Identification of possible loci of variable number of tandem repeats in Mycobacterium tuberculosis. Tuber Lung Dis, 2000. 80(2): 69-74.
28. Teichmann, S.A., et al., Fast assignment of protein structures to sequences using the intermediate sequence library PDB-ISL. Bioinformatics, 2000. 16(2): 117-24.
29. Worboys, M., GIS, a computing perspective. 1995, London; Bristol, PA: Taylor & Francis.
30. Worley, K.C., et al., BEAUTY-X: enhanced BLAST searches for DNA queries. Bioinformatics, 1998. 14(10): 890-1.
31. Zhang, J. and T.L. Madden, PowerBLAST: a new network BLAST application for interactive or automated sequence analysis and annotation. Genome Res, 1997. 7(6): 649-56.
32. Zhu, J., R. Luthy, and C.E. Lawrence, Database search based on Bayesian alignment. Proc Int Conf Intell Syst Mol Biol, 1999: 297-305.