메뉴 건너뛰기




Volumn 2, Issue 1, 2009, Pages 205-216

Reference-based alignment in large sequence databases

Author keywords

[No Author keywords available]

Indexed keywords

DATABASE SYSTEMS; QUERY PROCESSING;

EID: 79959936774     PISSN: None     EISSN: 21508097     Source Type: Conference Proceeding    
DOI: 10.14778/1687627.1687651     Document Type: Article
Times cited : (21)

References (44)
  • 4
    • 0017547820 scopus 로고
    • A fast string searching algorithm
    • R. S. Boyer and J. S. Moore. A fast string searching algorithm. Commun. ACM, 20(10):762-772, 1977.
    • (1977) Commun. ACM , vol.20 , Issue.10 , pp. 762-772
    • Boyer, R.S.1    Moore, J.S.2
  • 6
    • 0141717105 scopus 로고    scopus 로고
    • Better filtering with gapped q-grams
    • S. Burkhardt and J. Kärkkaäinen. Better filtering with gapped q-grams. Fundam. Inf., 56(1,2):51-70, 2002.
    • (2002) Fundam. Inf , vol.56 , Issue.1-2 , pp. 51-70
    • Burkhardt, S.1    Kärkkaäinen, J.2
  • 9
    • 84865098967 scopus 로고
    • Sublinear expected time approximate string matching and biological applications
    • Technical Report CSD-91-654, University of California at Berkeley
    • W. I. Chang and E. L. Lawler. Sublinear expected time approximate string matching and biological applications. Technical Report CSD-91-654, University of California at Berkeley, 1991.
    • (1991)
    • Chang, W.I.1    Lawler, E.L.2
  • 11
    • 0036306157 scopus 로고    scopus 로고
    • SST: an algorithm for finding near-exact sequence matches in time proportional to the logarithm of the database size
    • E. Giladi, M. G. Walker, J. Z. Wang, and W. Volkmuth. SST: an algorithm for finding near-exact sequence matches in time proportional to the logarithm of the database size. Bioinformatics, 18(6):873-877, 2002.
    • (2002) Bioinformatics , vol.18 , Issue.6 , pp. 873-877
    • Giladi, E.1    Walker, M.G.2    Wang, J.Z.3    Volkmuth, W.4
  • 12
    • 14644425852 scopus 로고
    • The smallest uniform upper bound on the distance between the mean and the median of the binomial and poisson distributions
    • K. Hamza. The smallest uniform upper bound on the distance between the mean and the median of the binomial and poisson distributions. Statistics and Probability Letters, 23(1):21-25, 1995.
    • (1995) Statistics and Probability Letters , vol.23 , Issue.1 , pp. 21-25
    • Hamza, K.1
  • 13
    • 0037314081 scopus 로고    scopus 로고
    • A generalized global alignment algorithm
    • X. Huang and K.-M. Chao. A generalized global alignment algorithm. Bioinformatics, 19(2):228-233, 2003.
    • (2003) Bioinformatics , vol.19 , Issue.2 , pp. 228-233
    • Huang, X.1    Chao, K.-M.2
  • 14
    • 0034139837 scopus 로고    scopus 로고
    • Jongeneel. Searching the expressed sequence tag (est) databases: Panning for genes
    • C. V. Jongeneel. Searching the expressed sequence tag (est) databases: Panning for genes. Bioinformatics, 1:76-92, 2000.
    • (2000) Bioinformatics , vol.1 , pp. 76-92
    • Jongeneel, C.V.1
  • 15
    • 1842667856 scopus 로고    scopus 로고
    • Pash: Efficient genome-scale sequence anchoring by positional hashing
    • K. J. Kalafus, A. R. Jackson, and A. Milosavljevic. Pash: Efficient genome-scale sequence anchoring by positional hashing. Genome Resources, 14(4):672678, 2004.
    • (2004) Genome Resources , vol.14 , Issue.4 , pp. 672678
    • Kalafus, K.J.1    Jackson, A.R.2    Milosavljevic, A.3
  • 16
    • 0022030599 scopus 로고
    • Efficient randomized pattern-matching algorithms
    • R. M. Karp and M. O. Rabin. Efficient randomized pattern-matching algorithms. IBM J. Res. Dev., 31(2):249-260, 1987.
    • (1987) IBM J. Res. Dev , vol.31 , Issue.2 , pp. 249-260
    • Karp, R.M.1    Rabin, M.O.2
  • 17
    • 84865078574 scopus 로고    scopus 로고
    • Resource BLAT-The BLAST-Like Alignment Tool
    • W. J. Kent. Resource BLAT-The BLAST-Like Alignment Tool. Genome Research, 2002.
    • (2002) Genome Research
    • Kent, W.J.1
  • 19
    • 23444433057 scopus 로고    scopus 로고
    • miblast: scalable evaluation of a batch of nucleotide sequence queries with blast
    • Y. J. Kim, A. Boyd, B. D. Athey, and J. M. Patel. miblast: scalable evaluation of a batch of nucleotide sequence queries with blast. Nucleic Acids Res, 33:4335-4344, 2005.
    • (2005) Nucleic Acids Res , vol.33 , pp. 4335-4344
    • Kim, Y.J.1    Boyd, A.2    Athey, B.D.3    Patel, J.M.4
  • 20
    • 0003352252 scopus 로고
    • The art of computer programming
    • D. E. Knuth. The art of computer programming. Sorting and Searching, 3, 1973.
    • (1973) Sorting and Searching , vol.3
    • Knuth, D.E.1
  • 21
    • 0034519012 scopus 로고    scopus 로고
    • Mpblast : improved blast performance with multiplexed queries
    • I. Korf and W. Gish. Mpblast : improved blast performance with multiplexed queries. Bioinformatics, 16:1052-1053, 2000.
    • (2000) Bioinformatics , vol.16 , pp. 1052-1053
    • Korf, I.1    Gish, W.2
  • 23
    • 0001116877 scopus 로고
    • Binary codes capable of correcting deletions, insertions, and reversals
    • V. I. Levenshtein. Binary codes capable of correcting deletions, insertions, and reversals. Soviet Physics, 10(8):707-710, 1966.
    • (1966) Soviet Physics , vol.10 , Issue.8 , pp. 707-710
    • Levenshtein, V.I.1
  • 25
    • 85011032600 scopus 로고    scopus 로고
    • improving performance of approximate queries on string collections using variable-length grams
    • C. Li, B. Wang, and X. Yang. Vgram: improving performance of approximate queries on string collections using variable-length grams. In International Conference on Very Large Data Bases (VLDB), pages 303-314, 2007.
    • (2007) International Conference on Very Large Data Bases (VLDB) , pp. 303-314
    • Li, C.1    Wang, B.2    Yang, X.3
  • 26
    • 0021919480 scopus 로고
    • Rapid and sensitive protein similarity searches
    • March
    • D. J. Lipman and W. R. Pearson. Rapid and sensitive protein similarity searches. Science, 227(4693):1435-1441, March 1985.
    • (1985) Science , vol.227 , Issue.4693 , pp. 1435-1441
    • Lipman, D.J.1    Pearson, W.R.2
  • 32
    • 84957654004 scopus 로고    scopus 로고
    • A new indexing method for approximate string matching
    • G. Navarro and R. Baeza-Yates. A new indexing method for approximate string matching. In Combinatorial Pattern Matching, 10th Annual Symposium, pages 163-185, 1999.
    • (1999) Combinatorial Pattern Matching , pp. 163-185
    • Navarro, G.1    Baeza-Yates, R.2
  • 33
    • 0014757386 scopus 로고
    • A general method applicable to the search for similarities in the amino acid sequence of two proteins
    • S. Needleman and C. Wunsch. A general method applicable to the search for similarities in the amino acid sequence of two proteins. Journal on Molecular Biology, 48(3):443-53, 1970.
    • (1970) Journal on Molecular Biology , vol.48 , Issue.3 , pp. 443-453
    • Needleman, S.1    Wunsch, C.2
  • 34
    • 0034764307 scopus 로고    scopus 로고
    • SSAHA: A fast search method for large dna databases
    • Z. Ning, A. J. Cox, and J. C. Mullikin. SSAHA: A fast search method for large dna databases. Genome Resources, 11(10):1725-1729, 2001.
    • (2001) Genome Resources , vol.11 , Issue.10 , pp. 1725-1729
    • Ning, Z.1    Cox, A.J.2    Mullikin, J.C.3
  • 35
    • 0023989064 scopus 로고
    • Improved tools for biological sequence comparison
    • April
    • W. R. Pearson and D. J. Lipman. Improved tools for biological sequence comparison. Proc Natl Acad Sci U S A, 85(8):2444-2448, April 1988.
    • (1988) Proc Natl Acad Sci U S A , vol.85 , Issue.8 , pp. 2444-2448
    • Pearson, W.R.1    Lipman, D.J.2
  • 38
    • 0017334283 scopus 로고
    • Similarity of the general designs of protochordates and invertebrates
    • G. J. Russell and J. H. Subak-Sharpe. Similarity of the general designs of protochordates and invertebrates. Nature, 266:533-536, 1977.
    • (1977) Nature , vol.266 , pp. 533-536
    • Russell, G.J.1    Subak-Sharpe, J.H.2
  • 39
    • 0019887799 scopus 로고
    • Identification of common molecular subsequences
    • T. F. Smith and M. S. Waterman. Identification of common molecular subsequences. Journal of Molecular Biology, 147:195-197, 1981.
    • (1981) Journal of Molecular Biology , vol.147 , pp. 195-197
    • Smith, T.F.1    Waterman, M.S.2
  • 40
    • 0020494998 scopus 로고
    • Algorithms for approximate string matching
    • E. Ukkonen. Algorithms for approximate string matching. Information Control, 64(1-3):100-118, 1985.
    • (1985) Information Control , vol.64 , Issue.1-3 , pp. 100-118
    • Ukkonen, E.1
  • 41
    • 0001704377 scopus 로고
    • On-line construction of suffix trees
    • E. Ukkonen. On-line construction of suffix trees. Algorithmica, 14(3):249-260, 1995.
    • (1995) Algorithmica , vol.14 , Issue.3 , pp. 249-260
    • Ukkonen, E.1
  • 43
    • 57149130672 scopus 로고    scopus 로고
    • Cost-based variable-length-gram selection for string collections to support approximate queries efficiently
    • X. Yang, B. Wang, and C. Li. Cost-based variable-length-gram selection for string collections to support approximate queries efficiently. In ACM International Conference on Management Of Data (SIGMOD), pages 353-364, 2008.
    • (2008) ACM International Conference on Management Of Data (SIGMOD) , pp. 353-364
    • Yang, X.1    Wang, B.2    Li, C.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.