메뉴 건너뛰기




Volumn 2, Issue 3, 2002, Pages 195-205

AGenDA: Gene prediction by comparative sequence analysis

Author keywords

Comparative genome analysis; Cross species sequence comparison; Dynamic programming; Gene prediction; Genome annotation; Phylogenetic footprinting; Sequence alignment

Indexed keywords

PROTEIN;

EID: 0036455972     PISSN: 13866338     EISSN: None     Source Type: Journal    
DOI: None     Document Type: Conference Paper
Times cited : (16)

References (34)
  • 1
    • 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. and Morgenstern, B. (2001). Speeding up the DIALIGN multiple alignment program by using the "Greedy Alignment of BIOlogical Sequences LIBrary" (GABIOS-LIB). Lecture Notes in Computer Science 2066, 1-11.
    • (2001) Lecture Notes in Computer Science , vol.2066 , pp. 1-11
    • Abdeddaïm, S.1    Morgenstern, B.2
  • 5
    • 0034565167 scopus 로고    scopus 로고
    • The conserved exon method for gene finding
    • Bafna, V. and Huson, D. H. (2000). The conserved exon method for gene finding. In: Proceedings ISMB 8, pp. 3-12.
    • (2000) Proceedings ISMB , vol.8 , pp. 3-12
    • 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., Mesirovi, J. P., Berger B. and Lander, E. S. (2000). Human and mouse gene structure: Comparative analysis and application to exon prediction. Genome Res. 7, 950-958.
    • (2000) Genome Res. , vol.7 , pp. 950-958
    • Batzoglou, S.1    Pachter, L.2    Mesirovi, J.P.3    Berger, B.4    Lander, E.S.5
  • 7
    • 0030628597 scopus 로고    scopus 로고
    • Dynamite: A exible code generating language for dynamic programming methods used in sequence comparison
    • Birney, E. and Durbin, R. (1997). Dynamite: A exible code generating language for dynamic programming methods used in sequence comparison. In: Proceedings ISMB 5, pp. 56-64.
    • (1997) Proceedings ISMB , vol.5 , pp. 56-64
    • Birney, E.1    Durbin, R.2
  • 8
    • 0031586003 scopus 로고    scopus 로고
    • Prediction of complete gene structures in human genomic DNA
    • Burge, C. and Karlin, S. (1997). Prediction of complete gene structures in human genomic DNA. J. Mol. Biol. 268, 78-94.
    • (1997) J. Mol. Biol. , vol.268 , pp. 78-94
    • Burge, C.1    Karlin, S.2
  • 9
    • 0030585734 scopus 로고    scopus 로고
    • Evaluation of gene structure prediction programs
    • Burset, M. and Guigó, R. (1996). Evaluation of gene structure prediction programs. Genomics 34, 353-367.
    • (1996) Genomics , vol.34 , pp. 353-367
    • Burset, M.1    Guigó, R.2
  • 10
    • 0034891211 scopus 로고    scopus 로고
    • The search for meaning in noncoding DNA
    • Clark, A. G. (2001). The search for meaning in noncoding DNA. Genome Res. 11, 1319-1320.
    • (2001) Genome Res. , vol.11 , pp. 1319-1320
    • Clark, A.G.1
  • 11
    • 0030768930 scopus 로고    scopus 로고
    • Computational methods for the identification of genes in vertebrate genomic sequences
    • Claverie, J.-M. (1997). Computational methods for the identification of genes in vertebrate genomic sequences. Hum. Mol. Genet. 6, 1735-1744.
    • (1997) Hum. Mol. Genet. , vol.6 , pp. 1735-1744
    • Claverie, J.-M.1
  • 14
    • 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
    • Göttgens, B., Gilbert, J. G. R., Barton, L. M., Grafham, D., Rogers, J., Bentley, D. R. and Green, A. R. (2001). 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) Genome Res. , vol.11 , pp. 87-97
    • Göttgens, 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
  • 16
    • 0033782834 scopus 로고    scopus 로고
    • An assessment of gene prediction accuracy in large DNA sequences
    • Guigó, R., Agarwal, P., Abril, J. F., Burset, M. and Fickett, J. W. (2000). An assessment of gene prediction accuracy in large DNA sequences. Genome Res. 10, 1631-1642.
    • (2000) Genome Res. , vol.10 , pp. 1631-1642
    • Guigó, R.1    Agarwal, P.2    Abril, J.F.3    Burset, M.4    Fickett, J.W.5
  • 18
    • 0030722935 scopus 로고    scopus 로고
    • Long human-mouse sequence alignments reveal novel regulatory elements: A reason to sequence the mouse genome
    • Hardison, R. C., Oeltjen J. and Miller, W. (1997). Long human-mouse sequence alignments reveal novel regulatory elements: A reason to sequence the mouse genome. Genome Res. 7, 959-966.
    • (1997) Genome Res. , vol.7 , pp. 959-966
    • Hardison, R.C.1    Oeltjen, J.2    Miller, W.3
  • 19
    • 0032884653 scopus 로고    scopus 로고
    • Comparative analysis of non- coding regions of 77 orthologous mouse and human gene pairs
    • Jareborg, N., Birney, E. and Durbin, R. (1999). Comparative analysis of non- coding regions of 77 orthologous mouse and human gene pairs. Genome Res. 9, 815-824.
    • (1999) Genome Res. , vol.9 , pp. 815-824
    • Jareborg, N.1    Birney, E.2    Durbin, R.3
  • 20
    • 0033832676 scopus 로고    scopus 로고
    • Conservation, regulation, synteny, and introns in a large-scale C. briggsae-C. elegans genomic alignment
    • Kent, W. J. and Zahler, A. M. (2000). Conservation, regulation, synteny, and introns in a large-scale C. briggsae-C. elegans genomic alignment. Genome Res. 10, 1115-1125.
    • (2000) Genome Res. , vol.10 , pp. 1115-1125
    • Kent, W.J.1    Zahler, A.M.2
  • 21
    • 17444437765 scopus 로고    scopus 로고
    • Integrating genomic homology into gene structure prediction
    • Korf, I., Flicek, P., Duan, D. and Brent, M. R. (2001). Integrating genomic homology into gene structure prediction. Bioinformatics 17, S140-S148.
    • (2001) Bioinformatics , vol.17
    • Korf, I.1    Flicek, P.2    Duan, D.3    Brent, M.R.4
  • 22
    • 0034616398 scopus 로고    scopus 로고
    • Identification of a coordinate regulator of interleukins 4, 13, and 5 by c ross-species sequence comparisons
    • Loots, G. G., Locksley, R. M., Blankespoor, C. M., Wang, Z. E., Miller, W., Rubin, E. M. and Frazer, K. A. (2000). Identification of a coordinate regulator of interleukins 4, 13, and 5 by c ross-species sequence comparisons. Science 288, 136-140.
    • (2000) Science , vol.288 , 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
  • 23
    • 0032519353 scopus 로고    scopus 로고
    • GeneMark.hmm: New solutions for gene finding
    • Lukashin, A. V. and Borodovsky, M. (1998). GeneMark.hmm: New solutions for gene finding. Nucleic Acids Res. 26, 1107-1115.
    • (1998) Nucleic Acids Res. , vol.26 , pp. 1107-1115
    • Lukashin, A.V.1    Borodovsky, M.2
  • 24
    • 0035011227 scopus 로고    scopus 로고
    • Comparison of genomic DNA sequences: Solved and unsolved problems
    • Miller, W. (2001). Comparison of genomic DNA sequences: Solved and unsolved problems. Bioinformatics 17, 391-397.
    • (2001) Bioinformatics , vol.17 , pp. 391-397
    • Miller, W.1
  • 25
    • 0029861894 scopus 로고    scopus 로고
    • Multiple DNA and protein sequence alignment based on segment-to-segment comparison
    • Morgenstern, B., Dress, A. and Werner, T. (1996). Multiple DNA and protein sequence alignment based on segment-to-segment comparison. Proc. Natl. Acad. Sci. U S A 93, 12098-12103.
    • (1996) Proc. Natl. Acad. Sci. U S A , vol.93 , pp. 12098-12103
    • Morgenstern, B.1    Dress, A.2    Werner, T.3
  • 26
    • 0032945593 scopus 로고    scopus 로고
    • DIALIGN 2: Improvement of the segment-to-segment approach to multiple sequence alignment
    • Morgenstern, B. (1999). DIALIGN 2: Improvement of the segment-to-segment approach to multiple sequence alignment. Bioinformatics 15, 211-218.
    • (1999) Bioinformatics , vol.15 , pp. 211-218
    • Morgenstern, B.1
  • 27
    • 0033636013 scopus 로고    scopus 로고
    • A space-efficient algorithm for aligning large genomic sequences
    • Morgenstern, B. (2000). A space-efficient algorithm for aligning large genomic sequences. Bioinformatics 16, 948-949.
    • (2000) Bioinformatics , vol.16 , pp. 948-949
    • Morgenstern, B.1
  • 29
    • 0035177648 scopus 로고    scopus 로고
    • Gene recognition in eukaryotic DNA by comparison of genomic sequences
    • Novichkov, P. S., Gelfand, M. S. and Mironov, A. A. (2001). Gene recognition in eukaryotic DNA by comparison of genomic sequences. Bioinformatics 17, 1011-1018.
    • (2001) Bioinformatics , vol.17 , pp. 1011-1018
    • Novichkov, P.S.1    Gelfand, M.S.2    Mironov, A.A.3
  • 30
    • 0030869663 scopus 로고    scopus 로고
    • A method for identifying splice sites and translational start sites in eukaryotic mRNA
    • Salzberg, S. L. (1997). A method for identifying splice sites and translational start sites in eukaryotic mRNA. Comput. Appl. Biosci. 13, 365-376.
    • (1997) Comput. Appl. Biosci. , vol.13 , pp. 365-376
    • Salzberg, S.L.1
  • 32
    • 0034069452 scopus 로고    scopus 로고
    • Gene-finding approaches for eukaryotes
    • Stormo, G. D. (2000). Gene-finding approaches for eukaryotes. Genome Res. 10, 394-397.
    • (2000) Genome Res. , vol.10 , pp. 394-397
    • Stormo, G.D.1
  • 33
    • 0026351408 scopus 로고
    • Locating protein-coding regions in human DNA sequences by a multiple sensor-neural network approach
    • Uberbacher, E. C. and Mural, R. J. (1991). Locating protein-coding regions in human DNA sequences by a multiple sensor-neural network approach. Proc. Natl. Acad. Sci. 88, 11261-11265.
    • (1991) Proc. Natl. Acad. Sci. , vol.88 , pp. 11261-11265
    • Uberbacher, E.C.1    Mural, R.J.2
  • 34
    • 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. and Guigó, R. (2001). SGP-1: Prediction and validation of homologous genes based on sequence alignments. Genome Research 11, 1574-1583.
    • (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.