메뉴 건너뛰기




Volumn 4, Issue , 2003, Pages

Fast and sensitive multiple alignment of large genomic sequences

Author keywords

[No Author keywords available]

Indexed keywords

ACCURACY; ARTICLE; COMPUTER PROGRAM; CONTROLLED STUDY; EXON; GENETIC ALGORITHM; GENOME ANALYSIS; LEUKEMIA; PROMOTER REGION; QUALITY CONTROL; SCORING SYSTEM; SENSITIVITY AND SPECIFICITY; SEQUENCE ALIGNMENT; SEQUENCE HOMOLOGY; STATISTICAL SIGNIFICANCE; TIME; ALGORITHM; ANIMAL; BIOLOGY; CHICKEN; COMPARATIVE STUDY; GENETICS; GENOME; HUMAN; MOUSE; PATHOLOGY; PROCEDURES; RAT; REGULATORY SEQUENCE; STATISTICS AND NUMERICAL DATA; STEM CELL; TETRAODONTIFORMES; TUMOR GENE; ZEBRA FISH;

EID: 2942603015     PISSN: 14712105     EISSN: None     Source Type: Journal    
DOI: 10.1186/1471-2105-4-66     Document Type: Article
Times cited : (127)

References (54)
  • 1
    • 0035011227 scopus 로고    scopus 로고
    • Comparison of genomic DNA sequences: Solved and unsolved problems
    • Miller W: Comparison of genomic DNA sequences: solved and unsolved problems. Bioinformatics 2001, 17:391-397.
    • (2001) Bioinformatics , vol.17 , pp. 391-397
    • Miller, W.1
  • 3
    • 0142056169 scopus 로고    scopus 로고
    • An applications-focused review of comparative genomics tools: Capabilities, limitations, and future challenges
    • Chain P, Kurtz S, Ohlebusch E, Slezak T: An applications-focused review of comparative genomics tools: capabilities, limitations, and future challenges. Briefings in Bioinformatics 2003, 4:105-123.
    • (2003) Briefings in Bioinformatics , vol.4 , pp. 105-123
    • Chain, P.1    Kurtz, S.2    Ohlebusch, E.3    Slezak, T.4
  • 5
    • 2942579268 scopus 로고    scopus 로고
    • The conserved exon method for gene finding
    • Bafna V, Huson DH: The conserved exon method for gene finding. Bioinformatics 2000, 16:190-202.
    • (2000) Bioinformatics , vol.16 , pp. 190-202
    • Bafna, V.1    Huson, D.H.2
  • 6
    • 0033861549 scopus 로고    scopus 로고
    • Human and mouse gene structure: Comparative analysis and application to exon prediction
    • Batzoglou S, Pachter L, Mesirov JP, Berger B, Lander ES: Human and mouse gene structure: comparative analysis and application to exon prediction. Genome Research 2000, 10(7):950-958.
    • (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
  • 7
    • 17444437765 scopus 로고    scopus 로고
    • Integrating genomic homology into gene structure prediction
    • Korf I, Flicek P, Duan D, Brent MR: Integrating genomic homology into gene structure prediction. Bioinformatics 2001:S140-S148.
    • (2001) Bioinformatics
    • Korf, I.1    Flicek, P.2    Duan, D.3    Brent, M.R.4
  • 8
    • 0034832202 scopus 로고    scopus 로고
    • SGP-1: Prediction and validation of homologous genes based on sequence alignments
    • Wiehe T, Gebauer-Jung S, Mitchell-Olds T, Guig ́R: SGP-1: Prediction and validation of homologous genes based on sequence alignments. Genome Research 2001, 11:1574-1583.
    • (2001) Genome Research , vol.11 , pp. 1574-1583
    • Wiehe, T.1    Gebauer-Jung, S.2    Mitchell-Olds, T.3    Guig, ́R.4
  • 9
    • 0036455972 scopus 로고    scopus 로고
    • AGenDA: Gene prediction by comparative sequence analysis
    • Rinner O, Morgenstern B: AGenDA: Gene prediction by comparative sequence analysis. In Silico Biology 2002, 2:195-205.
    • (2002) In Silico Biology , vol.2 , pp. 195-205
    • Rinner, O.1    Morgenstern, B.2
  • 11
    • 0031593199 scopus 로고    scopus 로고
    • Locus control regions of mammalian β-globin gene clusters: Combining phylo-genetic analyses and experimental results to gain functional insights
    • Hardison R, Slightom JL, Gumucio DL, Goodman M, Stojanovic N, Miller W: Locus control regions of mammalian β-globin gene clusters: combining phylo-genetic analyses and experimental results to gain functional insights. Gene 1998, 205:73-94.
    • (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
  • 12
    • 0032884653 scopus 로고    scopus 로고
    • Comparative analysis of noncoding regions of 77 orthologous mouse and human gene pairs
    • Jareborg N, Birney E, Durbin R: Comparative analysis of noncoding regions of 77 orthologous mouse and human gene pairs. Genome Research 1999, 9:815-824.
    • (1999) Genome Research , vol.9 , pp. 815-824
    • Jareborg, N.1    Birney, E.2    Durbin, R.3
  • 13
    • 0034616398 scopus 로고    scopus 로고
    • Identification of a coordinate regulator of interleukins 4, 13, and 5 by cross-species sequence comparisons
    • Loots GG, Locksley RM, Blankespoor CM, Wang ZE, Miller W, Rubin EM, Frazer KA: Identification of a coordinate regulator of interleukins 4, 13, and 5 by cross-species sequence comparisons. Science 2000, 288(5463):136-140.
    • (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
  • 16
    • 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
    • Gẗtgens B, Gilbert JGR, Barton LM, Grafham D, Rogers J, Bentley DR, Green AR: 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 2001, 11:87-97.
    • (2001) Genome Res. , vol.11 , pp. 87-97
    • Gẗtgens, B.1    Gilbert, J.G.R.2    Barton, L.M.3    Grafham, D.4    Rogers, J.5    Bentley, D.R.6    Green, A.R.7
  • 20
    • 0033066718 scopus 로고    scopus 로고
    • REPuter : Fast computation of maximal repeats in complete genomes
    • Kurtz S, Schleiermacher C: REPuter : Fast computation of maximal repeats in complete genomes. Bioinformatics 1999, 15(5):426-427.
    • (1999) Bioinformatics , vol.15 , Issue.5 , pp. 426-427
    • Kurtz, S.1    Schleiermacher, C.2
  • 24
    • 0032945593 scopus 로고    scopus 로고
    • DIALIGN 2: Improvement of the segment-to-segment approach to multiple sequence alignment
    • Morgenstern B: DIALIGN 2: improvement of the segment-to-segment approach to multiple sequence alignment. Bioinformatics 1999, 15:211-218.
    • (1999) Bioinformatics , vol.15 , pp. 211-218
    • Morgenstern, B.1
  • 25
    • 0032751751 scopus 로고    scopus 로고
    • Evolution of bhlh transcription factors: Modular evolution by domain shuffling?
    • Morgenstern B, Atchley WR: Evolution of bhlh transcription factors: modular evolution by domain shuffling? Mol Biol Evol 1999, 16:1654-1663.
    • (1999) Mol. Biol. Evol. , vol.16 , pp. 1654-1663
    • Morgenstern, B.1    Atchley, W.R.2
  • 26
    • 31244432403 scopus 로고    scopus 로고
    • A simple and space-efficient fragment-chaining algorithm for alignment of DNA and protein sequences
    • Morgenstern B: A simple and space-efficient fragment-chaining algorithm for alignment of DNA and protein sequences. Applied Mathematics Letters 2002, 15:11-16.
    • (2002) Applied Mathematics Letters , vol.15 , pp. 11-16
    • Morgenstern, B.1
  • 28
    • 18244404842 scopus 로고    scopus 로고
    • Fast and sensitive alignment of large genomic sequences
    • 14 - 16 August 2002; Paolo Alto Edited by: Vicky Markstein and Peter Markstein. IEEE Computer Society
    • Brudno M, Morgenstern B: Fast and sensitive alignment of large genomic sequences. In Proceedings IEEE Computer Society Bioinformatics Conference: 14 - 16 August 2002; Paolo Alto Edited by: Vicky Markstein and Peter Markstein. IEEE Computer Society; 2002:138-147.
    • (2002) Proceedings IEEE Computer Society Bioinformatics Conference , pp. 138-147
    • Brudno, M.1    Morgenstern, B.2
  • 29
    • 0029861894 scopus 로고    scopus 로고
    • Multiple DNA and protein sequence alignment based on segment-to-segment comparison
    • Morgenstern B, Dress AWM, Werner T: Multiple DNA and protein sequence alignment based on segment-to-segment comparison. Proc Natl Acad Sci USA 1996, 93:12098-12103.
    • (1996) Proc. Natl. Acad. Sci. USA , vol.93 , pp. 12098-12103
    • Morgenstern, B.1    Dress, A.W.M.2    Werner, T.3
  • 30
    • 23044525766 scopus 로고    scopus 로고
    • Speeding up the DIALIGN multiple alignment program by using the 'greedy alignment of biological sequences library' (GABIOS-LIB)
    • Abdeddaïm S, Morgenstern B: Speeding up the DIALIGN multiple alignment program by using the 'greedy alignment of biological sequences library' (GABIOS-LIB). Lecture Notes in Computer Science 2001, 2066:1-11.
    • (2001) Lecture Notes in Computer Science , vol.2066 , pp. 1-11
    • Abdeddaïm, S.1    Morgenstern, B.2
  • 31
    • 0028341506 scopus 로고
    • Comparative analysis of multiple protein-sequence alignment methods
    • McClure MA, Vasi TK, Fitch WM: Comparative analysis of multiple protein-sequence alignment methods. Mol Biol Evol 1994, 11:571-592.
    • (1994) Mol. Biol. Evol. , vol.11 , pp. 571-592
    • McClure, M.A.1    Vasi, T.K.2    Fitch, W.M.3
  • 32
    • 0032988850 scopus 로고    scopus 로고
    • BAliBASE: A benchmark alignment database for the evaluation of multiple sequence alignment programs
    • Thompson JD, Plewniak F, Poch O: BAliBASE: A benchmark alignment database for the evaluation of multiple sequence alignment programs. Bioinformatics 1999, 15:87-88.
    • (1999) Bioinformatics , vol.15 , pp. 87-88
    • Thompson, J.D.1    Plewniak, F.2    Poch, O.3
  • 33
    • 0037010180 scopus 로고    scopus 로고
    • Quality assessment of multiple alignment programs
    • Lassmann T, Sonnhammer ELL: Quality assessment of multiple alignment programs. FEBS Letters 2002, 529:126-130.
    • (2002) FEBS. Letters , vol.529 , pp. 126-130
    • Lassmann, T.1    Sonnhammer, E.L.L.2
  • 34
    • 0033135847 scopus 로고    scopus 로고
    • The SCL gene: From case report to critical hematopoietic regulator
    • Begley CG, Green AR: The SCL gene: from case report to critical hematopoietic regulator. Blood 1999, 93:2760-2770.
    • (1999) Blood , vol.93 , pp. 2760-2770
    • Begley, C.G.1    Green, A.R.2
  • 36
    • 0030932424 scopus 로고    scopus 로고
    • Distinct mechanisms direct SCL/TAL-1 expression in erythroid cells and CD34 positive primitive myeloid cells
    • Bockamp EO, McLaughlin F, Göttgens B, Murrell AM, Elefanty AG, Green AR: Distinct mechanisms direct SCL/TAL-1 expression in erythroid cells and CD34 positive primitive myeloid cells. J Biol Chem 1997, 272:8781-8790.
    • (1997) J. Biol. Chem. , vol.272 , pp. 8781-8790
    • Bockamp, E.O.1    McLaughlin, F.2    Göttgens, B.3    Murrell, A.M.4    Elefanty, A.G.5    Green, A.R.6
  • 38
    • 0344061505 scopus 로고    scopus 로고
    • Distinct 5′ SCL enhancers direct transcription to developing brain, spinal cord, and endothelium: Neural expression is mediated by GATA factor binding sites
    • Sinclair AM, Gẗtgens B, Barton LM, Stanley ML, Pardanaud L, Klaine M, Bahn MGS, Sanchez M, Bench AJ: Distinct 5′ SCL enhancers direct transcription to developing brain, spinal cord, and endothelium: neural expression is mediated by GATA factor binding sites. Dev Biol 1999, 209:128-142.
    • (1999) Dev. Biol. , vol.209 , pp. 128-142
    • Sinclair, A.M.1    Gẗtgens, B.2    Barton, L.M.3    Stanley, M.L.4    Pardanaud, L.5    Klaine, M.6    Bahn, M.G.S.7    Sanchez, M.8    Bench, A.J.9
  • 39
    • 0027964907 scopus 로고
    • GATA-and SP1-binding sites are required for the full activity of the tissue-specific promoter of the TAL-1 gene
    • Lecointe N, Bernard O, Naert K, Joulin V, Larsen JC, Romeo PH, Mathieu-Mahul D: GATA-and SP1-binding sites are required for the full activity of the tissue-specific promoter of the TAL-1 gene. Oncogene 1994, 9:2623-2632.
    • (1994) Oncogene , vol.9 , pp. 2623-2632
    • Lecointe, N.1    Bernard, O.2    Naert, K.3    Joulin, V.4    Larsen, J.C.5    Romeo, P.H.6    Mathieu-Mahul, D.7
  • 40
    • 0028807522 scopus 로고
    • DNA binding sites for the transcriptional activator/repressor YY1
    • Hyde-DeRuyscher RP, Jennings E, Shenk T: DNA binding sites for the transcriptional activator/repressor YY1. Nuc Acids Res 1995, 23:4457-4465.
    • (1995) Nuc. Acids Res. , vol.23 , pp. 4457-4465
    • Hyde-DeRuyscher, R.P.1    Jennings, E.2    Shenk, T.3
  • 41
    • 0042121222 scopus 로고    scopus 로고
    • MAVID multiple alignment server
    • Bray N, Pachter L: MAVID multiple alignment server. Nucleic Acids Research 2003, 31:3525-3526.
    • (2003) Nucleic Acids Research , vol.31 , pp. 3525-3526
    • Bray, N.1    Pachter, L.2
  • 42
    • 0037398368 scopus 로고    scopus 로고
    • LAGAN and multi-LAGAN: Efficient tools for large-scale multiple alignment of genomic DNA
    • NISC Sequencing Consortium, Green ED, Sidow A, Batzoglou S
    • Brudno M, Do C, Cooper G, Kim MF, Davydov E, NISC Sequencing Consortium, Green ED, Sidow A, Batzoglou S: LAGAN and multi-LAGAN: Efficient tools for large-scale multiple alignment of genomic DNA. Genome Research 2003, 13:721-731.
    • (2003) Genome Research , vol.13 , pp. 721-731
    • Brudno, M.1    Do, C.2    Cooper, G.3    Kim, M.F.4    Davydov, E.5
  • 45
    • 0036107903 scopus 로고    scopus 로고
    • Discovery of regulatory elements by a computational method for phylogenetic footprinting
    • Blanchette M, Tompa M: Discovery of regulatory elements by a computational method for phylogenetic footprinting. Genome Research 2002, 12:739-748.
    • (2002) Genome Research , vol.12 , pp. 739-748
    • Blanchette, M.1    Tompa, M.2
  • 48
    • 0023989064 scopus 로고
    • Improved tools for biological sequence comparison
    • Pearson WR, Lipman DJ: Improved tools for biological sequence comparison. Proc Natl Acad Sci USA 1988, 85:2444-2448.
    • (1988) Proc. Natl. Acad. Sci. USA , vol.85 , pp. 2444-2448
    • Pearson, W.R.1    Lipman, D.J.2
  • 49
    • 0034883255 scopus 로고    scopus 로고
    • Analysis of conserved noncoding dna in drosophila reveals similar constraints in intergenic and intronic sequences
    • Bergman CM, Kreitman M: Analysis of conserved noncoding dna in drosophila reveals similar constraints in intergenic and intronic sequences. Genome Research 2001, 11:1335-1345.
    • (2001) Genome Research , vol.11 , pp. 1335-1345
    • Bergman, C.M.1    Kreitman, M.2
  • 50
    • 0035958930 scopus 로고    scopus 로고
    • An IgH enhancer that drives transcription through basic helix-loop-helix and Oct transcription factor binding motifs. Functional analysis of the E(mu)3′ enhancer of the catfish
    • Cioffi CC, Middleton DL, Wilson MR, Miller NW, Clem LW, Warr GW: An IgH enhancer that drives transcription through basic helix-loop-helix and Oct transcription factor binding motifs. Functional analysis of the E(mu)3′ enhancer of the catfish. J Biol Chem 2001, 276:27825-27830.
    • (2001) J. Biol. Chem. , vol.276 , pp. 27825-27830
    • Cioffi, C.C.1    Middleton, D.L.2    Wilson, M.R.3    Miller, N.W.4    Clem, L.W.5    Warr, G.W.6
  • 51
    • 0031857684 scopus 로고    scopus 로고
    • Rose: Generating sequence families
    • Stoye J, Evers D, Meyer F: Rose: Generating sequence families. Bioinformatics 1998, 14:157-163.
    • (1998) Bioinformatics , vol.14 , pp. 157-163
    • Stoye, J.1    Evers, D.2    Meyer, F.3
  • 52
    • 0016518897 scopus 로고
    • Efficient string matching: An aid to bibliographic search
    • Aho A, Corasick M: Efficient string matching: an aid to bibliographic search. Comm ACM 1975, 18:333-340.
    • (1975) Comm. ACM , vol.18 , pp. 333-340
    • Aho, A.1    Corasick, M.2
  • 53
    • 84945709825 scopus 로고
    • Trie memory
    • Fredkin E: Trie memory. Comm ACM 1960, 3:490-500.
    • (1960) Comm. ACM , vol.3 , pp. 490-500
    • Fredkin, E.1
  • 54
    • 0025436383 scopus 로고
    • Skip lists: A probabilistic alternative to balanced trees
    • Pugh W: Skip lists: A probabilistic alternative to balanced trees. Comm ACM 1990, 33:668-676.
    • (1990) Comm. ACM , vol.33 , pp. 668-676
    • Pugh, W.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.