Survey on index based homology search algorithms

Journal of Supercomputing

Volumn 40, Issue 2, 2007, Pages 185-212

  Jiang, Xianyang ^a,b   Zhang, Peiheng ^b   Liu, Xinchun ^b   Yau, Stephen S T ^c,d  

^a CAMPUS DE BEAULIEU   (France)

^b INSTITUTE OF COMPUTING TECHNOLOGY   (China)

^c UNIVERSITY OF ILLINOIS AT CHICAGO   (United States)

^d EAST CHINA NORMAL UNIVERSITY   (China)

Author keywords

Algorithm; Bioinformatics; Genomic indexing; Homology search; Sequence alignment

Indexed keywords

BIOINFORMATICS; CLASSIFICATION (OF INFORMATION); INDEXING (OF INFORMATION); SEARCH ENGINES;

GENOMIC INDEXING; HOMOLOGY SEARCH; INDEX BASED HOMOLOGY; SEARCH ALGORITHMS; SEQUENCE ALIGNMENT;

ALGORITHMS;

EID: 34147142480     PISSN: 09208542     EISSN: 15730484     Source Type: Journal    
DOI: 10.1007/s11227-006-0041-0     Document Type: Article

References (38)

1. Aghili SA, Agrawal D, El Abbadi A (2003) Filtration of string proximity search via transformation. In: Third IEEE symposium on bioinformatics and bioengineering (BIBE'03), Bethesda, MD, USA, 2003
2. Aghili SA, Sahin OD, Agrawal D, El Abbadi A (2004) Efficient filtration of sequence similarity search through singular value decomposition. In: Fourth IEEE symposium on bioinformatics and bioengineering (BIBE'04), Taichung, Taiwan, 2004
3. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ (1990) Basic local alignment search tool. National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD
4. Altschul SF, Madden T, Alejandro A, Schaffer A, Zhang J, Zhang Z, Miller W, Lipman DJ (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, July 1997
5. Argyros T, Ermopoulos C (2003) Efficient subsequence matching in time series databases under time and amplitude transformations. In: ICDM, 2003, pp 481-484
6. Califano A, Rigoutsos I (1993) FLASH: a fast look-up algorithm for string homology. In: International conference on intelligent systems for molecular biology, Bethesda, MD, pp 56-64
7. Cao X, Li SC, Ooi BC, Tung AKH (2004) Piers: an efficient model for similarity search in DNA sequence databases. Sigmod Record, Special Issue
8. Chattaraj A, Williams HE (2004) Variable-length intervals in homology search. In: Asia-pacific bioinformatics conference, Dunedin, New Zealand, 2004
9. Chen W, Aberer K (1997) Efficient querying on genomic databases by using metric space indexing techniques. Technical Report No. 1056, German National Research Center for Information Technology
10. Chen W, Aberer K (1997) Efficient querying on genomic databases by using metric space indexing techniques. In: Eighth international conference and workshop on database and expert-systems applications (DEXA'97), Toulouse, France
11. Cooper G, Raymer M, Doom T, Krane D, Futamur N (2004) Indexing genomic databases. In: Fourth IEEE symposium on bioinformatics and bioengineering (BIBE'04), Taichung, Taiwan, 2004
12. Fondrat C, Dessen P (1995) A Rapid access motif database (RAMdb) with a search algorithm for the retrieval patterns in nucleic acids or protein databanks. Comput Appl Biosci 11(3):273-279
13. Gardner-Stephen P, Knowles G (2003) A novel architecture for genomic sequence searching and alignment. In: Asia-pacific computer systems architecture conference, pp 180-192
14. Hobohm U, Sander C (1995) A sequence property approach to searching protein databases. J Molec Biol 251:390-399
15. Hunt E, Atkinson MP, Irving RW (2001) A database index to large biological sequences. In: Proceedings of the 27th VLDB conference, Roma, Italy, 2001
16. Hunt E, Atkinson MP, Irving RW (2002) Database indexing for large DNA and protein sequence collections. VLDB J 11(3):256-271
17. Kahveci T, Singh AK (2001) An efficient index structure for string databases. In: Proceedings of the 37th VLDB conference, Roma, Italy, 2001
18. Kahveci T, Singh AK (2003) MAP: searching large genome databases. In: Pacific symposium on biocomputing, Hawai, 2003
19. Kailing K, Kriegel H-P, Schonauer S, Seidl T (2004) Efficient similarity search for hierarchical data in large databases. In: Proc 9th int conf on extending database technology (EDBT 2004), Heraklion, Greece, pp 676-693
20. Kent WJ (2002) BLAT: the BLAST-like alignment too. Genom Res 12(4)
21. Kriegel H-P, Schonauer S (2003) Similarity search in structured data. In: Proc 5th int conf on data warehousing and knowledge discovery (DaWaK'03), Prague, Czech Republic, Lecture notes in computer science (LNCS), vol 2737, 2003, pp 309-319
22. Lee HP, Tsai YT, Sheu TF, Tang CT (2004) An IDC-based algorithm for efficient homology filtration with guaranteed seriate coverage. In: Fourth IEEE symposium on bioinformatics and bioengineering (BIBE'04), Taichung, Taiwan, 2004
23. Navarro G, Baeza-Yates R, Sutinen E, Tarhio J (2001) Indexing methods for approximate string matching. IEEE Data Eng Bul 24(4)
24. Ning Z, Cox AJ, Mulikin JC (2001) A fast search method for large DNA databases. Genom Res 11(10)
25. Oliver T, Schmidt B (2004) High performance biosequence database scanning on reconfigurable platforms. In: IPDPS04 (HiCOMB), Santa Fe, NM, IEEE, 2004
26. Ong TH, Tan KL, Wang H (2002) Indexing genomic databases for fast homology searching. In: Proceedings of the 13th international conference on database and expert systems applications, September 2002, Aix-en-Provence, France, pp 871-880
27. Ooi BC, Pang HH, Wang H, Wong L, Yu C (2002) Fast filter-and-refine algorithms for subsequence selection. In: Proceedings of the 6th international database engineering and applications symposium (IDEAS'02), Edmonton, Canada, July 2002, pp 243-254
28. Ozturk O, Ferhatosmanoglu H (2003) Effective indexing and filtering for similarity search in large biosequence databases. In: 3rd IEEE international symposium on bioinformatics and bioengineering (BIBE 2003), Bethesda, MD, USA
29. Pearson WR, Lipman DJ (1988) Improved tools for biological sequence comparison. Proc Natl Acad Sci USA 85:2444-2448
30. Rognes T, Seeberg E (1998) SALSA: improved protein database searching by a new algorithm for assembly of sequence fragments into gapped alignments. Bioinf 14(10):839-845
31. Roy A, Mullick A, Genomic indexing using wavelets. Available at: http://people.csa.iisc.ernet.in/~aroy/gene.doc
32. Seshadri P, Livny M, et al (1996) The design and implementation of a sequence database system. In: Proc of the 22nd VLDB conf, Mumbai, India
33. Shamir R (1998) Algorithms for molecular biology, Lecture 3. Tel Aviv University, Fall 1998
34. Willams HE (1997) Fast ranking strategies for genomic databases
35. Williams HE (1999) Effective query filtering for fast homology searching. In: Pacific symposium on biocomputing, Hawaii, pp 214-225
36. Williams H, Zobel J (1996) Indexing nucleotide databases for fast query evaluation. In: Proc of the 5th international conference on extending database technology, Avignon, France, pp 275-288
37. Williams H, Zobel J (2002) Indexing and retrieval for genomic databases. IEEE Trans Knowl Data Eng 14(1):63-78
38. Yang Y, Liu B, Zhang Z (2003) Partition based hierarchical index for text retrieval. In: WAIM, 2003, pp 161-172