An efficient similarity search based on indexing in large DNA databases

Computational Biology and Chemistry

Volumn 34, Issue 2, 2010, Pages 131-136

  Jeong, In Seon ^a   Park, Kyoung Wook ^a   Kang, Seung Ho ^a   Lim, Hyeong Seok ^a  

^a Chonnam National University   (South Korea)

Author keywords

Approximate string matching; DNA sequence; Indexing; Similarity search

Indexed keywords

APPROXIMATE STRING MATCHING; DNA DATABASE; DNA SEQUENCE DATABASE; INDEX STRUCTURE; MULTIDIMENSIONAL VECTORS; POSITIONAL INFORMATION; QUERY SEQUENCE; RUNTIMES; SEARCH ALGORITHMS; SIMILARITY SEARCH;

DNA; DNA SEQUENCES; GENES; HAMMING DISTANCE; INDEXING (OF INFORMATION); LEARNING ALGORITHMS; VECTOR SPACES; WAVELET TRANSFORMS;

HEURISTIC ALGORITHMS;

ALGORITHM; ARTICLE; HUMAN; INFORMATION RETRIEVAL; NUCLEIC ACID DATABASE; NUCLEOTIDE SEQUENCE; SEQUENCE HOMOLOGY;

ALGORITHMS; BASE SEQUENCE; DATABASES, NUCLEIC ACID; HUMANS; INFORMATION STORAGE AND RETRIEVAL; SEQUENCE HOMOLOGY;

EID: 77953289693     PISSN: 14769271     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.compbiolchem.2010.03.007     Document Type: Article

References (15)

1. Altschul S.F., Gish W., Miller W., Myers E.W., and Lipman D.J. Basic local alignment search tool. J. Mol. Biol. 215 (1990) 403-410
2. 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
3. Cao X., Li S.C., Ooi B.C., and Tung A.K.H. Piers: an efficient model for similarity search in DNA sequence databases. ACM SIGMOD Rec. 33 (2004) 39-44
4. Gusfield D. Algorithms on Strings, Trees, and Sequences. Computer Science and Computational Biology. 1th ed. (1997), Cambridge University Press, New York
5. Guttman A. R-Trees, a dynamic index structure for spatial searching. ACM SIGMOD Rec. (1984) 47-57
6. Jeong I.S., Park K.W., and Lim H.S. A fast heuristic algorithm for similarity search in large DNA databases. Proc. FBIT Int. Conf. (2007) 335-340
7. Jiang X., Zhang P., and Liu X. Survey on index based homology search algorithms. J. Supercomput. 40 (2007) 185-212
8. Kahveci T., and Singh A.K. An efficient index structure for string databases. Proc. VLDB Int. Conf. (2001) 351-360
9. Kang S.H., Choi M.H., Jeong I.S., and Lim H.S. An efficient two-phase algorithm to find gene-specific probes for large genomes. Proc. FBIT Int. Conf. (2007) 205-210
10. Ma B., Tromp J., and Li M. PatternHunter: faster and more sensitive homology search. Bioinformatics 18 (2002) 440-445
11. Mount D.W. Bioinformatics: Sequence and Genome Analysis (2001), Cold Spring Harbor Laboratory Press, New York
12. Ozturk O., and Ferhatosmanoglu H. Effective indexing and filtering for similarity search in large biosequence database. Proc. IEEE BIBE (2003) 359-366
13. Smith T.F., and Waterman M.S. Identification of common molecular subsequences. J. Mol. Biol. 147 (1981) 195-197
14. Webb-Robertson B.J., Oehmen C.S., and Shah A.R. A feature vector integration approach for a generalized support vector machine pairwise homology algorithm. Comput. Biol. Chem. 32 (2008) 458-461
15. Williams H.E., and Zobel J. Indexing and retrieval for genomic databases. IEEE TKDE 14 (2002) 63-78