The ed-tree: An index for large DNA sequence databases

Proceedings of the International Conference on Scientific and Statistical Database Management, SSDBM

Volumn 2003-January, Issue , 2003, Pages 151-160

  Tan, Zhenqiang ^a   Cao, Xia ^a   Ooi, Beng Chin ^a   Tung, A K H ^a  

^a NATIONAL UNIVERSITY OF SINGAPORE   (Singapore)

Author keywords

Bioinformatics; Computer science; Databases; DNA; Genomics; Indexes; Probes; Q measurement; Search methods; Sequences

Indexed keywords

BIOINFORMATICS; COMPUTER SCIENCE; DATABASE SYSTEMS; DIGITAL STORAGE; DNA; DNA SEQUENCES; FORESTRY; LEARNING ALGORITHMS; MANAGEMENT INFORMATION SYSTEMS; NUCLEIC ACIDS; PROBES; QUERY PROCESSING;

GENOMICS; INDEXES; Q MEASUREMENTS; SEARCH METHOD; SEQUENCES;

TREES (MATHEMATICS);

EID: 84872065533     PISSN: 10993371     EISSN: None     Source Type: Conference Proceeding    
DOI: 10.1109/SSDM.2003.1214976     Document Type: Conference Paper

References (12)

1. J. Buhler. Efficient large-scale sequence comparison by locality-sensitive hashing. Bioinformatics, 17:419-428, 2001.
2. S. Burkhardt, A. Crauser, P. Ferragina, H. P. Lenhof, and M. Vingron. q-gram based database searching using a suffix array (quasar). In Int. Conf. RECOMB, Lyon, April 1999.
3. E. Giladi, M. Walker, J. Wang, and W. Volkmuth. Sst: An algorithm for searching sequence databases in time proportional to the logarithm of the database size. In Int. Conf. RECOMB, Japan, 2000.
4. R. S. C. Goble, P. Baker, and A. Brass. A classification of tasks in bioinformatics. Bioinformatics, 17:180-188, 2001.
5. E. Hunt, M. P. Atkinson, and R. W. Irving. A database index to large biological sequences. In International Journal on VLDB, pages 139-148, Roma, Italy, September 2001.
6. T. Kahveci and A. Singh. An efficient index structure for string databases. In Int. Conf. VLDB, Roma, Italy, 2001.
7. K.Sadakane and T.Shibuya. Indexing huge genome sequences for solving various problems. Genome Informatics, pages 175-183, 2001.
8. B. Ma, J. Tromp, and M. Li. Patternhunter: faster and more sensitive homology search. Bioinformatics, 18:440-445, 2002.
9. S.F.Altschul, W.Gish, W.Miller, E.W.Myers, and D.J.Lipman. Basic local alignment search tool. Molecular Biology, 215:403-410, 1990.
10. D. J. States and P. Agarwal. Compact encoding strategies for dna sequence similarity search. In ISMB, 1996.
11. T.F.Smith and M.S.Waterman. Identification of common molecular subsequences. Molecular Biology, 147:195-197, 1981.
12. H.E. Williams and J.Zobel. Indexing and retrieval for genomic databases. IEEE Transactions on Knowledge and Data Engineering, 14:63-78, 2002.