On integrating peptide sequence analysis and relational distance-based indexing

Proceedings - Sixth IEEE Symposium on BioInformatics and BioEngineering, BIBE 2006

Volumn , Issue , 2006, Pages 27-34

  Xu, Weijia ^a   Mao, Rui ^a   Wang, Shu ^b   Mitanker, Daniel P ^a  

^a Institute of Advanced Computer Science   (United States)

^b The University of Texas at Austin   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ALPHABET SIZE; COMPUTATIONAL COSTS; DIMENSIONALITY; METRIC-DISTANCE; SUBSTITUTION MATRIX;

COMPUTER PROGRAMMING; DATABASE SYSTEMS; HAMMING DISTANCE; INDEXING (MATERIALS WORKING); INFORMATION MANAGEMENT; MATHEMATICAL MODELS; SCALABILITY;

PEPTIDES;

EID: 34547438633     PISSN: None     EISSN: None     Source Type: Conference Proceeding    
DOI: 10.1109/BIBE.2006.253312     Document Type: Conference Paper

References (46)

1. S.F. Altschul, W. Gish, W.Miller, E. W. Myers & D. J. Lipman Basic local alignment search tool J. Mol. Biol., 215:403-410 1990
2. G. Bejerano, M. Pheasant, I. Makunin, S. Stephen, W.J. Kent, J.S. Mattick, D. Haussler, "Ultraconserved elements in the human genome," Science. 304(5675):1321-5. 2004
3. R. Bellman Adaptive Control Processes: A Guided Tour, Princeton University Press. New Jersey, U.S. 1961
4. D. A. Benson, I. Karsch-Mizrachi, D.J. Lipman, J. Ostell & D.L. Wheeler "GenBank" Ncl. Aci. Res. 1:D34-8 2005
5. T. Bozkaya & M. Ozsoyoglu Indexing Large Metric Spaces for Similarity Search Queries. ACM Transactions on Database System, 24(3):361-404 1999
6. Hjaltason, G. R. & Samet, H. "Index-driven similarity search in metric spaces" ACM Transactions on Database Systems 28(4), 517-580, 2003
7. B. Chazelle. Computational geometry: a retrospective. in Proc. ACM STOC'94, pages 75-94, 1994.
8. B. Eckman "Efficient Access to BLAST using IBM DB2 Information Integrator" IBM health care & life sciences Sep. 2004.
9. M.O. Dayhoff, R. Schwartz & B.C. Orcutt Atlas of Protein Sequence and Structure. 5:(3):345-358 1978
10. H. Garcia-Molina, J. Ullman, & J. Widom. Database Systems: The Complete Book, Prentice Hall, 2nd, 2001
11. E. Giladi, G. M.Walker, J.Z.Wang, & W. Volkmuth SST: an algorithm for finding near-exact sequence matches in time proportional to the logarithm of the database size. Bioinformatic. 18(6):873-879 2002
12. M. Gribskov & N.L. Robinson Use of receiver operating characteristic (ROC) analysis to evaluate sequence matching. Computers and Chemistry. 20(1):25-33 1996
13. D. Gusfield Algorithms on Strings, Trees and Sequences Computer Science and Computational Biology. 449-454 Press Syndicate of the University of Cambridge, USA 1997
14. A. Guttman. R-trees: A Dynamic Index Structure for Spatial Searching. Proc. of SIGMOD, 1984.
15. E. Halperin, J.Buhler, R. Karp, R. Krauthgamer, and B. Westover Detecting Protein Sequences Via Metric Embeddings In Proceedings of the 11th ISMB 122-199, Brisbane, Australia, Jun. 29-Jul. 03, 2003
16. S. Henikoff, and J.G. Henikoff Amino acid substitution matrices fromprotein blocks. Proc. Natl. Acad. Sci. USA 89, 10915-10919 1992
17. M. Linial, N. Linial, N. Tishby, & G. Yona "Global self organization of all known protein sequences reveals inherent biological signatures" J. Mol. Bio. 268:539-556 1997
18. R. Krauthgamer and J. R. Lee The black-box complexity of nearest neighbor search. in Proc. Of Int. Coll ICALP Turku, Finland, July 12-16 2004
19. V. Kumar and V. N. Rao "Parallel depth first search. part II. analysis" International Journal of Parallel Programming, vol. 16, no. 6, pp. 501-519, 1987
20. R. Mao, W. Xu, S. Ramakrishnan, G. Nuckolls, & D. Miranker "On Optimizing Distance-Based Similarity Search for Biological Databases" in Proc. of CSB 2005: 351-361
21. T. P. Mann & W. S. Noble "Efficient Identification of DNA Binding Partners in a Sequence Database" Bioinformatics 22(14):e350-8 2006
22. E.M. Marcotte, M. Pellegrini, H.L. Ng, D.W. Rice, T.O. Yeates and D. Eisenberg, "Detecting protein function and protein-protein interactions from genome sequences," Science. 285(5428):751-3. 1999
23. th VLDB Conference, 910-921, Berlin, Germany, Sep. 9-12, 2003
24. D.P. Miranker, W.J. Briggs, R. Mao, S. Ni and W. Xu Biosequence Use Cases in MoBIoS SQL, Data Engineering Bulletin, 27(3): 3-11 2004
25. E Murphy, I Rigoutsos, T Shibuya, and T E. Shenk Reevaluation of human cytornegalovirus coding potential PNAS 100: 13585-13590, 2003
26. E.W. Myers, A sublinear algorithm for approximate keyword searching. Algorithmica. 12(4/5):345-374 1994
27. S.B. Needleman & C.D. Wunsch An efficient method applicable to the search for similarities in the amino acid sequences of two proteins. J. Mol. Biol. 48, 443-453 1970
28. D.A. Patterson & J.L.Hermessy "Computer Architecture A Quantitative Approach" Morgan Kaufmann 1996
29. M. J. Pazzani, J. Muramatsu, and D. Billsus "Syskill & webert: Identifying interesting web sites" in proceeding of AAAI/IAAI'96, pages 54-61, 1996.
30. V. J. Promponas, A.J. Eriright, S.Tsoka, D.P. Kreil, C.Leroy, S.J. Hamodrakas, C.Sander & C.A.Ouzounis, CAST: an iterative algorithm for the complexity analysis of sequence tracts Bioinformatics 16:915-922 2000
31. S R Ramakrishnan, R Mao, A A Nakorchevskiy, J T Prince, W S Willard, W Xu, E M Marcotte, and D P Miranker. "A fast coarse filtering method for protein
32. identification by mass spectrometry" Bioinformatics, 22 (12): 1524, 2006
33. E. C.Rouchka, W.Gish, & D. J. States Comparison of whole genome assemblies of the human genome. Nucleic Acids Res., 30(22):5004-5014 2002
34. A.A. Schaffer, L.Aravin, T. L.Madden, S.Shavirin, J. L.Spouge, Y. I. Wolf, E.V.Koonin & Altschul, S.F. Improving the accuracy of PSI-BLAST protein database searches with composition-based statistics and other refinements. Nucleic Acids Res., 29(14):2994-3005 2001
35. P.H. Sellers On the theory and computation of evolutionary distances. J. Appl. Math. 26:787-793 1974
36. S. Shekhar & S. Chawla Spatial Databases: A Tour, Prentice Hall, USA 2002
37. S.M. Stephens, J.Y.Chen, M.G.Davidson, S.Thomas, B.M.Trute "Oracle Database 10g: a platform for BLAST search and Regular Expression pattern matching in life sciences" Nucl. Acids Res. 33: D675-679 2005
38. W. R. Taylor & D. T. Jones Deriving an amino acid matrix. J. Theor. Biol. 164, 65-83 1993
39. J.C. Wootton & S. Federhen (1993) Statistics of local complexity in amino acid sequences and sequence databases Comput. Chem. 17:149-163.
40. S. Wu, U. Manber, G. Myers, and W. Miller An O(NP) Sequence Comparison Algorithm. Information Processing Letters 35(6): 317-323 1990
41. W. Xu & D.P. Mirauker A metric model for amino acid substitution Bioinformatics 20(8):1214-21 2004
42. W. Xu, W.J. Briggs, J. Padolina, W. Liu, C.R. Linder, and D.P. Miranker, "Using MoBIoS' Scalable Genome Joins to Find Conserved Primer Pair Candidates Between Two Genomes" Bioinfoimatics 20: i355-i362. 2004
43. W. Xu, D.P. Miranker, R. Mao, & S. Wang Indexing Protein Sequences in Metric Space, Univ. Texas at Austin, Dept. of Comp. Sci. TR-04-062004
44. P. Yianilos Locally Lifting the Curse of Dimensionality for Nearest Neighbor Search, In Proc. ACM-SIAM Symposium on Discrete Algorithms, Jan. 9-11, 2000, San Francisco, California 2000
45. H. Yu, NM Luscombe, HX Lu, X Zhu, Y Xia, JD Han, N Bertin, S Chung, M Vidal, M Gerstein Annotation transfer between genomes: protein-protein interologs and protein-DNA regulogs Genome Res 14:1107-18 2004
46. Z. Zhang and M. Gerstein "Of mice and men: phylogenetic footprinting aids the discovery of regulatory elements" Journal of Biology 2:11, 2003