Multi-sorting algorithm for finding pairs of similar short substrings from large-scale string data

Knowledge and Information Systems

Volumn 25, Issue 2, 2010, Pages 229-251

  Uno, Takeaki ^a  

^a NATIONAL INSTITUTE OF INFORMATICS   (Japan)

Author keywords

Data analysis; Homology search; Large scale data; Neighbor graph construction; Neighbor search; Similarity analysis

Indexed keywords

DATA REDUCTION; EFFICIENCY; GENETIC ENGINEERING; HAMMING DISTANCE; POLYNOMIAL APPROXIMATION;

HOMOLOGY SEARCH; LARGE SCALE DATA; NEIGHBOR GRAPH; NEIGHBOR SEARCHES; SIMILARITY ANALYSIS;

DATABASE SYSTEMS;

EID: 78049450664     PISSN: 02191377     EISSN: 02193116     Source Type: Journal    
DOI: 10.1007/s10115-009-0271-6     Document Type: Article

References (22)

1. Abrahamson K (1987) Generalized string matching. SIAM J Comput 16: 1039-1051.
2. Altschul FS, Gish W, Miller W, Myers EW, Lipman DJ (1990) Basic local alignment search tool. J Mol Biol 215: 403-410.
3. Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25: 3389-3402.
4. Amir A, Lewenstein M, Porat E (2000) Faster algorithms for string matching with k mismatches. In: Symposium on discrete algorithms, pp 794-803.
5. Assent I, Krieger R, Glavic B, Seidl T (2008) Clustering multidimensional sequences in spatial and temporal databases. Knowl Inf Syst 16: 29-51.
6. Brown P, Botstein D (2000) Exploring the new world of the genome with DNA microarrays. Nat Genet 21: 33-37.
7. Faloutsos C, Barber R, Flickner M, Hafner J, Niblack W, Petkovic D, Equitz W (1994) Efficient and effective querying by image content. Intell Inf Syst 3: 231-262.
8. Feigenbaum J, Kannan S, Strauss M, Viswanathan M (1999) An approximate L1-difference algorithm for massive data streams. In: Proceedings of FOCS99.
9. Fleischmann RD, Adams MD, White O, Clayton RA (1995) Whole-genome random sequencing and assembly of Haemophilus influenzae Rd. Science 28: 496-512.
10. Johnson DS, Mortazavi A, Myers RM, Wold B (2007) Genome-wide mapping of in vivo protein-DNA interactions. Science 31: 1441-1442.
11. Kawahara D, Kurohashi S (2006) Case frame compilation from the web using high-performance computing. In: Proceedings of the 5th international conference on language resources and evaluation (LREC2006), pp 1344-1347.
12. Koga H, Ishibashi T, Watanabe T (2007) Fast agglomerative hierarchical clustering algorithm using locality-sensitive hashing. Knowl Inf Syst 12: 25-53.
13. Liu J, Goss S, Murray G (1994) Similarity comparison and analysis of sequential data. In: IEEE international conference on expert systems for development, pp 138-143.
14. Manber U, Myers G (1993) Suffix arrays: a new method for on-line string searches. SIAM J Comput 22: 935-948.
15. Muthukrishnan S, Sahinalp SC (2000) Approximate nearest neighbors and sequence comparison with block operations. In: Proceedings of 32nd annual ACM symposium on theory of computing, pp 416-424.
16. Muthukrishnan S, Sahinalp SC (2002) Simple and practical sequence nearest neighbors under block edit operations. In: Proceedings of CPM2002.
17. Pearson WR (2000) Flexible sequence similarity searching with the FASTA3 program package. Methods Mol Biol 132: 185-219.
18. Popendorf K, Osana Y, Hachiya T, Sakakibara Y (2007) Murasaki-homology detection across multiple large-scale genomes. In: Fifth annual RECOMB satellite workshop on comparative genomics (San Diego, USA, 2007).
19. Shivakumar N, Garcia-Molina H (1996) Building a scalable and accurate copy detection mechanism. In: International conference on digital libraries, proceedings of the first ACM international conference on digital libraries, pp 160-168.
20. Yamada S, Gotoh O, Yamana H (2006) Improvement in accuracy of multiple sequence alignment using novel group-to-group sequence alignment algorithm with piecewise linear gap cost. BMC Bioinform 7: 524.
21. Yamada T, Morishita S (2003) Computing highly specific and mismatch tolerant oligomers efficiently. Bioinformatics Conference 2003.
22. Yamada T, Morishita S (2005) Accelerated off-target search algorithm for siRNA. Bioinformatics 21: 1316-1324.