Approximate substring matching over uncertain strings

Proceedings of the VLDB Endowment

Volumn 4, Issue 11, 2011, Pages 772-782

  Ge, Tingjian ^a   Li, Zheng ^a  

^a UNIVERSITY OF KENTUCKY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

INDEXING (OF INFORMATION); INFORMATION MANAGEMENT; PROBABILITY DISTRIBUTIONS;

BIOLOGICAL SEQUENCE DATA; FILTERING TECHNIQUE; INTRIGUING QUESTIONS; MATCHING QUERY; MATCHINGS; MULTILEVEL FILTERING; PROBABILITY: DISTRIBUTIONS; SUB-STRINGS; TEXT DATA; UNCERTAINTY;

SEMANTICS;

EID: 84862695811     PISSN: None     EISSN: 21508097     Source Type: Journal    
DOI: 10.14778/3402707.3402717     Document Type: Conference Paper

References (17)

1. C. Cantor, C. Smith. Genomics: The Science and Technology Behind the Human Genome Project. Wiley, 1999.
2. S. Chaudhuri, V. Ganti, R. Kaushik. A primitive operator for similarity joins in data cleaning. In ICDE, pages 5-16, 2006.
3. S. Dash, K. Chon, S. Lu, E. Raeder. Automatic Real Time Detection of Atrial Fibrillation. In Ann Biomed Eng., 37(9), pp. 1701-9, 2009.
4. B. Ewing et al.. Base-calling of automated sequencer traces using phred I accuracy assessment. In Genome Res., 8(3):175-85, 1998.
5. L. Gravano et al. Approximate string joins in a database (almost) for free. In VLDB, pages 491-500, 2001.
6. J. Jestes, F. Li, Z. Yan, K. Yi. Probabilistic String Similarity Joins. In SIGMOD, pages 327-338, 2010.
7. R. Kandhan, N. Teletia and J. M. Patel. SigMatch: Fast and Scalable Multi-Pattern Matching. In PVLDB, 3(1), pages 1173-1184, 2010.
8. M. Kircher, J. Kelso. High-throughput DNA sequencing - concepts and limitations. In BioEssays, 32, pages 524-536, 2010.
9. C. Li, J. Lu, Y. Lu. Efficient Merging and Filtering Algorithms for Approximate String Searches. In ICDE, pages 257-266, 2008.
10. G. Navarro. A Guided Tour to Approximate String Matching. In ACM Computing Surveys, Vol. 33, No. 1, pages 31-88, 2001.
11. G. Navarro et al. Indexing Methods for Approximate String Matching. In IEEE Data Eng. Bulletin, Vol. 24, No. 4, pages 19-27, 2001.
12. G. Navarro, L. Salmela. Indexing Variable Length Substrings for Exact and Approximate Matching. In SPIRE, pages 214-221, 2009.
13. Nomenclature Committee of the International Union of Biochemistry (NC-IUB). Nomenclature for incompletely specified bases in nucleic acid sequences. In Biochem J., 229(2), pages 281-6, 1985.
14. S. Tata, J. M. Patel, J. Friedman, A. Swaroop. Declarative Querying for Biological Sequences. In ICDE, pages 87-98, 2006.
15. The U. of Michigan DNA Sequencing Core. Interpretation of Sequencing Chromatograms. http://seqcore.brcf.med.umich.edu/
16. E. Ukkonen. Finding approximate patterns in strings. In Journal of Algorithms, 6, pages 132-137, 1985.
17. http://www.ncbi.nlm.nih.gov/Traces/home/.