메뉴 건너뛰기




Volumn , Issue , 2002, Pages 138-147

Fast and sensitive alignment of large genomic sequences

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHMS; BIOINFORMATICS; CHAINS; GENES;

EID: 18244404842     PISSN: None     EISSN: None     Source Type: Conference Proceeding    
DOI: 10.1109/CSB.2002.1039337     Document Type: Conference Paper
Times cited : (45)

References (33)
  • 1
    • 0016518897 scopus 로고
    • Efficient string matching: An aid to bibliographic search
    • A. Aho and M. Corasick. Efficient string matching: an aid to bibliographic search. Comm. ACM, 18:333-340, 1975.
    • (1975) Comm. ACM , vol.18 , pp. 333-340
    • Aho, A.1    Corasick, M.2
  • 3
    • 0034565167 scopus 로고    scopus 로고
    • The conserved exon method for gene finding
    • R. Altmann, T. Bailey, P. Bourne, M. Gribskov, T. Lengauer, I. Shindyalov, L. T. Eyck, and H. Weissig, editors, Menlo Parc, CA, AAAI Press
    • V. Bafna and D. H. Huson. The conserved exon method for gene finding. In R. Altmann, T. Bailey, P. Bourne, M. Gribskov, T. Lengauer, I. Shindyalov, L. T. Eyck, and H. Weissig, editors, Proceedings of the 8th International Conference on Intelligent Systems for Molecular Biology, Menlo Parc, CA, 2000. AAAI Press.
    • (2000) Proceedings of the 8th International Conference on Intelligent Systems for Molecular Biology
    • Bafna, V.1    Huson, D.H.2
  • 4
    • 0033861549 scopus 로고    scopus 로고
    • Human and mouse gene structure: Comparative analysis and application to exon prediction
    • S. Batzoglou, L. Pachter, J. P. Mesirov, B. Berger, and E. S. Lander. Human and mouse gene structure: comparative analysis and application to exon prediction. Genome Research, 10(7):950-958, 2000.
    • (2000) Genome Research , vol.10 , Issue.7 , pp. 950-958
    • Batzoglou, S.1    Pachter, L.2    Mesirov, J.P.3    Berger, B.4    Lander, E.S.5
  • 5
    • 0034883255 scopus 로고    scopus 로고
    • Analysis of conserved noncoding dna in drosophila reveals similar constraints in intergenic and intronic sequences
    • C. M. Bergman and M. Kreitman. Analysis of conserved noncoding dna in drosophila reveals similar constraints in intergenic and intronic sequences. Genome Research, 11:1335-1345, 2001.
    • (2001) Genome Research , vol.11 , pp. 1335-1345
    • Bergman, C.M.1    Kreitman, M.2
  • 7
    • 0036107903 scopus 로고    scopus 로고
    • Discovery of reguatory elements by a computational method for phylogenetic footprinting. Algorithms for phylogenetic footprinting
    • M. Blanchette and M. Tompa. Discovery of reguatory elements by a computational method for phylogenetic footprinting. Algorithms for phylogenetic footprinting. Genome Research, 12(5):739-48, 2002.
    • (2002) Genome Research , vol.12 , Issue.5 , pp. 739-748
    • Blanchette, M.1    Tompa, M.2
  • 9
    • 84945709825 scopus 로고
    • Trie memory
    • E. Fredkin. Trie memory. Comm. ACM, 3:490-500, 1960.
    • (1960) Comm. ACM , vol.3 , pp. 490-500
    • Fredkin, E.1
  • 13
    • 0035154384 scopus 로고    scopus 로고
    • Long-range comparison of human and mouse SCL loci: Localized regions of sensitivity to restriction endonucleases correspond precisely with peaks of conserved noncoding sequences
    • B. Göttgens, J. Gilbert, L. Barton, D. Grafham, J. Rogers, D. Bentley, and A. Green. Long-range comparison of human and mouse SCL loci: localized regions of sensitivity to restriction endonucleases correspond precisely with peaks of conserved noncoding sequences. Genome Res., 11:87-97, 2001.
    • (2001) Genome Res. , vol.11 , pp. 87-97
    • Göttgens, B.1    Gilbert, J.2    Barton, L.3    Grafham, D.4    Rogers, J.5    Bentley, D.6    Green, A.7
  • 15
    • 0031593199 scopus 로고    scopus 로고
    • Locus control regions of mammalian β-globin gene clusters: Combining phylogenetic analyses and experimental results to gain functional insights
    • R. Hardison, J. L. Slightom, D. L. Gumucio, M. Goodman, N. Stojanovic, and W. Miller. Locus control regions of mammalian β-globin gene clusters: combining phylogenetic analyses and experimental results to gain functional insights. Gene, 205:73-94, 1998.
    • (1998) Gene , vol.205 , pp. 73-94
    • Hardison, R.1    Slightom, J.L.2    Gumucio, D.L.3    Goodman, M.4    Stojanovic, N.5    Miller, W.6
  • 16
    • 0016518550 scopus 로고
    • A linear space algorithm for computing maximal common subsequences
    • D. S. Hirschberg. A linear space algorithm for computing maximal common subsequences. Commun. ACM, 18:314-343, 1975.
    • (1975) Commun. ACM , vol.18 , pp. 314-343
    • Hirschberg, D.S.1
  • 17
    • 0032884653 scopus 로고    scopus 로고
    • Comparative analysis of noncoding regions of 77 orthologous mouse and human gene pairs
    • N. Jareborg, E. Birney, and R. Durbin. Comparative analysis of noncoding regions of 77 orthologous mouse and human gene pairs. Genome Research, 9:815-824, 1999.
    • (1999) Genome Research , vol.9 , pp. 815-824
    • Jareborg, N.1    Birney, E.2    Durbin, R.3
  • 18
    • 0027175241 scopus 로고
    • Applications and statistics for multiple high-scoring segments in molecular sequences
    • S. Karlin and S. F. Altschul. Applications and statistics for multiple high-scoring segments in molecular sequences. Proc. Natl. Acad. Sci. USA, 90:5873-5877, 1993.
    • (1993) Proc. Natl. Acad. Sci. USA , vol.90 , pp. 5873-5877
    • Karlin, S.1    Altschul, S.F.2
  • 19
    • 0033832676 scopus 로고    scopus 로고
    • Conservation, regulation, synteny, and introns in a large-scale C. briggsae-C. elegans genomic alignment
    • W. J. Kent and A. M. Zahler. Conservation, regulation, synteny, and introns in a large-scale C. briggsae-C. elegans genomic alignment. Genome Research, 10(8):1115-1125, 2000.
    • (2000) Genome Research , vol.10 , Issue.8 , pp. 1115-1125
    • Kent, W.J.1    Zahler, A.M.2
  • 20
    • 17444437765 scopus 로고    scopus 로고
    • Integrating genomic homology into gene structure prediction
    • I. Korf, P. Flicek, D. Duan, and M. R. Brent. Integrating genomic homology into gene structure prediction. Bioinformatics, (17):S140-S148, 2001.
    • (2001) Bioinformatics , Issue.17 , pp. S140-S148
    • Korf, I.1    Flicek, P.2    Duan, D.3    Brent, M.R.4
  • 22
    • 0033066718 scopus 로고    scopus 로고
    • REPuter: Fast computation of maximal repeats in complete genomes
    • S. Kurtz and C. Schleiermacher. REPuter: Fast computation of maximal repeats in complete genomes. Bioinformatics, 15(5):426-427, 1999.
    • (1999) Bioinformatics , vol.15 , Issue.5 , pp. 426-427
    • Kurtz, S.1    Schleiermacher, C.2
  • 23
    • 0034616398 scopus 로고    scopus 로고
    • Identification of a coordinate regulator of interleukins 4, 13, and 5 by cross-species sequence comparisons
    • G. G. Loots, R. M. Locksley, C. M. Blankespoor, Z. E. Wang, W. Miller, E. M. Rubin, and K. A. Frazer. Identification of a coordinate regulator of interleukins 4, 13, and 5 by cross-species sequence comparisons. Science, 288(5463):136-140, 2000.
    • (2000) Science , vol.288 , Issue.5463 , pp. 136-140
    • Loots, G.G.1    Locksley, R.M.2    Blankespoor, C.M.3    Wang, Z.E.4    Miller, W.5    Rubin, E.M.6    Frazer, K.A.7
  • 24
    • 0032945593 scopus 로고    scopus 로고
    • DIALIGN 2: Improvement of the segment-to-segment approach to multiple sequence alignment
    • B. Morgenstern. DIALIGN 2: improvement of the segment-to-segment approach to multiple sequence alignment. Bioinformatics, 15:211-218, 1999.
    • (1999) Bioinformatics , vol.15 , pp. 211-218
    • Morgenstern, B.1
  • 25
    • 31244432403 scopus 로고    scopus 로고
    • A simple and space-efficient fragment-chaining algorithm for alignment of DNA and protein sequences
    • B. Morgenstern. A simple and space-efficient fragment-chaining algorithm for alignment of DNA and protein sequences. Applied Mathematics Letters, 15:11-16, 2002.
    • (2002) Applied Mathematics Letters , vol.15 , pp. 11-16
    • Morgenstern, B.1
  • 26
    • 0029861894 scopus 로고    scopus 로고
    • Multiple DNA and protein sequence alignment based on segment-to-segment comparison
    • B. Morgenstern, A. W. M. Dress, and T. Werner. Multiple DNA and protein sequence alignment based on segment-to-segment comparison. Proc. Natl. Acad. Sci. USA, 93:12098-12103, 1996.
    • (1996) Proc. Natl. Acad. Sci. USA , vol.93 , pp. 12098-12103
    • Morgenstern, B.1    Dress, A.W.M.2    Werner, T.3
  • 28
    • 0023989064 scopus 로고
    • Improved tools for biological sequence comparison
    • W. R. Pearson and D. J.Lipman. Improved tools for biological sequence comparison. Proc. Natl. Acad. Sci. USA, 85:2444-2448, 1988.
    • (1988) Proc. Natl. Acad. Sci. USA , vol.85 , pp. 2444-2448
    • Pearson, W.R.1    Lipman, D.J.2
  • 29
    • 0025436383 scopus 로고
    • Skip lists: Skip lists: A probabilistic alternative to balanced trees
    • W. Pugh. Skip lists: Skip lists: A probabilistic alternative to balanced trees. Comm ACM, 33:668-676, 1990.
    • (1990) Comm ACM , vol.33 , pp. 668-676
    • Pugh, W.1
  • 30
    • 0036455972 scopus 로고    scopus 로고
    • AGenDA: Gene prediction by comparative sequence analysis
    • O. Rinner and B. Morgenstern. AGenDA: Gene prediction by comparative sequence analysis. In Silico Biology, 2:0018, 2002
    • (2002) Silico Biology , vol.2 , pp. 18
    • Rinner, O.1    Morgenstern, B.2
  • 32
    • 0345676554 scopus 로고    scopus 로고
    • Multiple sequence alignment with the divide-and-conquer method
    • J. Stoye. Multiple sequence alignment with the divide-and-conquer method. Gene, 211:GC45-GC56, 1998.
    • (1998) Gene , vol.211 , pp. GC45-GC56
    • Stoye, J.1
  • 33
    • 0034832202 scopus 로고    scopus 로고
    • SGP-1: Prediction and validation of homologous genes based on sequence alignments
    • T. Wiehe, S. Gebauer-Jung, T. Mitchell-Olds, and R. Guigó. SGP-1: Prediction and validation of homologous genes based on sequence alignments. Genome Research, 11:1574-1583, 2001.
    • (2001) Genome Research , vol.11 , pp. 1574-1583
    • Wiehe, T.1    Gebauer-Jung, S.2    Mitchell-Olds, T.3    Guigó, R.4


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.