Indexing schemes for similarity search in datasets of short protein fragments

Information Systems

Volumn 32, Issue 8, 2007, Pages 1145-1165

  Stojmirović, Aleksandar ^a   Pestov, Vladimir ^a  

^a UNIVERSITY OF OTTAWA   (Canada)

Author keywords

Indexing; Protein fragments; Quasi metrics; Similarity search

Indexed keywords

ALGORITHMS; AMINO ACIDS; COMPUTATIONAL GEOMETRY; INDEXING (MATERIALS WORKING); PROTEINS;

PROTEIN FRAGMENTS; QUASI-METRICS; SIMILARITY SEARCH;

INFORMATION SYSTEMS;

EID: 34548513988     PISSN: 03064379     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.is.2007.03.001     Document Type: Article

References (57)

1. Hunt E., Atkinson M.P., and Irving R.W. A database index to large biological sequences. VLDB J. 11 3 (2001) 139-148
2. Hunt E. Indexed searching on proteins using a suffix sequoia. IEEE Data Eng. Bull. 27 (2004) 24-31
3. Buhler J. Efficient large-scale sequence comparison by locality-sensitive hashing. Bioinformatics 17 (2001) 419-428
4. Giladi E., Walker M.G., Wang J.Z., and Volkmuth W. SST: an algorithm for finding near-exact sequence matches in time proportional to the logarithm of the database size. Bioinformatics 18 6 (2002) 873-877
5. R. Mao, W. Xu, N. Singh, D.P. Miranker, An assessment of a metric space database index to support sequence homology, in: Third IEEE International Symposium on BioInformatics and BioEngineering (BIBE 2003), Bethesda, Maryland, March 2003, pp. 375-384.
6. Kent W.J. BLAT-the BLAST-like alignment tool. Genome Res. 12 4 (2002) 656-664
7. Z. Tan, X. Cao, B.C. Ooi, A.K.H. Tung, The ed-tree: an index for large DNA sequence databases, in: SSDBM, 2003, pp. 151-160.
8. Dayhoff M.O., Schwartz R.M., and Orcutt B.C. A model of evolutionary change in proteins. In: Dayhoff M.O. (Ed). Atlas of Protein Sequence and Structure vol. 5 (1978), National Biomedical Research Foundation 345-352 (Chapter 22)
9. Henikoff S., and Henikoff J.G. Amino acid substitution matrices from protein blocks. Proc. Natl. Acad. Sci. USA 89 (1992) 10915-10919
10. Ukkonen E. Approximate string matching with q-grams and maximal matches. Theoretical Computer Science 92 1 (1992) 191-211
11. Martin-Serrano J., Zang T., and Bieniasz P.D. HIV-1 and Ebola virus encode small peptide motifs that recruit Tsg101 to sites of particle assembly to facilitate egress. Nat. Med. 7 (2001) 1313-1319
12. Kitts D.D., and Weiler K. Bioactive proteins and peptides from food sources. Applications of bioprocesses used in isolation and recovery. Curr. Pharm. Des. 9 (2003) 1309-1323
13. Pestov V., and Stojmirović A. Indexing schemes for similarity search: an illustrated paradigm. Fund. Inf. 70 (2006) 367-385
14. Needleman S.B., and Wunsch C.D. A general method applicable to the search for similarities in the amino acid sequence of two proteins. J. Mol. Biol. 48 (1970) 443-453
15. Smith T.F., and Waterman M.S. Identification of common molecular subsequences. J. Mol. Biol. 147 (1981) 195-197
16. Gribskov M., McLachlan A.D., and Eisenberg D. Profile analysis: detection of distantly related proteins. Proc. Natl. Acad. Sci. USA 84 (1987) 4355-4358
17. Altschul S.F., Madden T.L., Schaffer A.A., Zhang J., Zhang Z., Miller W., and Lipman D.J. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25 (1997) 3389-3402
18. Künzi H.-P.A. Nonsymmetric distances and their associated topologies: about the origins of basic ideas in the area of asymmetric topology. Handbook of the History of General Topology, History of Topology vol. 3 (2001), Kluwer Academic Publishers, Dordrecht 853-968
19. Stojmirović A. Quasi-metric spaces with measure. Topology Proc. 28 2 (2004) 655-671
20. Künzi H.-P.A., and Vajner V. Weighted quasi-metrics. Papers on General Topology and Applications (1994), Flushing, NY, New York Academy of Science, New York 64-77
21. Vitolo P. The representation of weighted quasi-metric spaces. Rend. Istit. Mat. Univ. Trieste 31 1-2 (1999) 95-100
22. Chavez E., Navarro G., Baeza-Yates R.A., and Marroquin J.L. Searching in metric spaces. ACM Comput. Surv. 33 3 (2001) 273-321
23. Hjaltason G.R., and Samet H. Index-driven similarity search in metric spaces. ACM Trans. Database Syst. 28 4 (2003) 517-580
24. T.K. Sellis, N. Roussopoulos, C. Faloutsos, The R + - tree: a dynamic index for multi-dimensional objects, in: Proceedings of 13th International Conference on Very Large Data Bases (VLDB'87), Brighton, England, September 1987, pp. 507-518.
25. K.S. Beyer, J. Goldstein, R. Ramakrishnan, U. Shaft, When is "nearest neighbor" meaningful?, in: Proceedings of Seventh International Conference on Database Theory (ICDT'99), Jerusalem, Israel, January 1999, pp. 217-235.
26. Pestov V. On the geometry of similarity search: dimensionality curse and concentration of measure. Inf. Process. Lett. 73 (2000) 47-51
27. M. Gromov, Metric Structures for Riemannian and non-Riemannian Spaces, Progress in Mathematics, vol. 152, Birkhäuser, Base, 1999.
28. M. Ledoux, The Concentration of Measure Phenomenon, Mathematical Surveys and Monographs, vol. 89, American Mathematical Society, 2001.
29. P. Ciaccia, M. Patella, P. Zezula, M-tree: an efficient access method for similarity search in metric spaces, in: Proceedings of 23rd International Conference on Very Large Data Bases (VLDB'97), Athens, Greece, August 1997, pp. 426-435.
30. T. Bozkaya, Z.M. Özsoyoglu, Distance-based indexing for high-dimensional metric spaces, in: Proceedings of the 1997 ACM SIGMOD International Conference on Management of Data, Tucson, Arizona, May 1997, pp. 357-368.
31. Ciaccia P., Patella M., and Zezula P. Processing complex similarity queries with distance-based access methods. In: Schek H.-J., Saltor F., Ramos I., and Alonso G. (Eds). Proceedings of the Sixth International Conference on Extending Database Technology (EDBT'98) Valencia, Spain, March 1998 (1998), Springer, Berlin 9-23
32. Ciaccia P., and Patella M. Searching in metric spaces with user-defined and approximate distances. ACM Trans. Database Syst. 27 4 (2002) 398-437
33. P.N. Yianilos, Data structures and algorithms for nearest neighbor search in general metric spaces, in: Proceedings of the Fourth Annual ACM/SIGACT-SIAM Symposium on Discrete Algorithms, Austin, Texas, January 1993.
34. Fredkin E. Trie memory. Commun. ACM 3 9 (1960) 490-499
35. Morrison D.R. Patricia-practical algorithm to retrieve information coded in alphanumeric. J. ACM 15 4 (1968) 514-534
36. P. Weiner, Linear pattern matching algorithms, in: Proceedings of the 14th Annual Symposium on Switching and Automata Theory, IEEE, 1973, pp. 1-11.
37. McCreight E.M. A space-economical suffix tree construction algorithm. J. ACM 23 2 (1976) 262-272
38. E. Ukkonen, Constructing suffix trees on-line in linear time, in: Proceedings of the IFIP 12th World Computer Congress on Algorithms, Software, Architecture-Information Processing '92, vol. 1, Madrid, Spain, September 1992, pp. 484-492.
39. Gusfield D. Algorithms on Strings, Trees, and Sequences-Computer Science and Computational Biology (1997), Cambridge University Press, Cambridge
40. Kurtz S. Reducing the space requirements of suffix trees. Software Pract. Exp. 29 13 (1999) 1149-1171
41. Manber U., and Myers E.W. Suffix arrays: a new method for on-line string searches. SIAM J. Comput. 22 5 (1993) 935-948
42. Gonnet G.H., Cohen M.A., and Benner S.A. Exhaustive matching of the entire protein sequence database. Science 256 (1992) 1443-1445
43. Smith R.F., and Smith T.S. Automatic generation of primary sequence patterns from sets of related protein sequences. Proc. Natl. Acad. Sci. USA 87 (1990) 118-122
44. H.H. Seward, Information sorting in the application of electronic digital computers to business operations, Master's Thesis, MIT, 1954.
45. Hoare C.A.R. Quicksort, Comput. J. 5 (1962) 10-15
46. Sjölander K., Karplus K., Brown M., Hughey R., Krogh A., Mian I.S., and Haussler D. Dirichlet mixtures: a method for improving detection of weak but significant protein sequence homology. Comput. Appl. Biosci. 12 4 (1996) 327-345
47. Durbin R., Eddy S., Krogh A., and Mitchison G. Biological Sequence Analysis (1998), Cambridge University Press, Cambridge, UK
48. Park J., Holm L., Heger A., and Chothia C. RSDB: representative protein sequence databases have high information content. Bioinformatics 16 5 (2000) 458-464
49. Wheeler D.L., Church D.M., Edgar R., Federhen S., Helmberg W., Madden T.L., Pontius J.U., Schuler G.D., Schriml L.M., Sequeira E., Suzek T.O., Tatusova T.A., and Wagner L. Database resources of the National Center for Biotechnology Information: update. Nucleic Acids Res. 32 Database issue (2004) D35-D40
50. Boeckmann B., Bairoch A., Apweiler R., Blatter M.-C., Estreicher A., Gasteiger E., Martin M.J., Michoud K., O'Donovan C., Phan I., Pilbout S., and Schneider M. The SWISS-PROT protein knowledgebase and its supplement TrEMBL in 2003. Nucleic Acids Res. 31 1 (2003) 365-370
51. Z. Bi, C. Faloutsos, F. Korn, The "DGX" distribution for mining massive, skewed data, in: Proceedings of the Seventh ACM SIGKDD International Conference on Knowledge Discovery and Data Mining, San Francisco, California, August 2001, pp. 17-26.
52. P. Ciaccia, M. Patella, Bulk loading the M-tree, in: Proceedings of the 9th Australasian Database Conference (ADC'98), Perth, Australia, February 1998, pp. 15-26.
53. T. Kahveci, A.K. Singh, An efficient index structure for string databases, in: Proceedings of the 2001 VLDB Conference, pp. 351-360.
54. A. Bhattacharya, T. Can, T. Kahveci, A.K. Singh, Y.-F. Wang, ProGreSS: simultaneous searching of protein databases by sequence and structure, in: Proceedings of the 2004 Pacific Symposium on Biocomputing, pp. 264-275.
55. S. Burkhardt, J. Kinen, Better filtering with gapped q-grams, in: Combinatorial Pattern Matching, 2001, pp. 73-85.
56. Navarro G., and Baeza-Yates R. A hybrid indexing method for approximate string matching. J. Discret. Algorithms 1 1 (2000) 205-239
57. Navarro G., Baeza-Yates R.A., Sutinen E., and Tarhio J. Indexing methods for approximate string matching. IEEE Data Eng. Bull. 24 4 (2001) 19-27