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Volumn 14, Issue 3, 2004, Pages 264-272

Recent advances in gene structure prediction

Author keywords

EHMM; EST; Evolutionary HMM; Expressed sequence tag; Hidden Markov model; HMM; Indels; Insertions and deletions; Open reading frame; ORF; Poly pyrimidine tract; PPT; Reverse transcription polymerase chain reaction; RT PCR; Transcription start sites; TSS; UTR

Indexed keywords

ARABIDOPSIS; CAENORHABDITIS ELEGANS; EUKARYOTE; EXON; GENE MUTATION; GENE SEQUENCE; GENE STRUCTURE; GENOME; HUMAN; NONHUMAN; PREDICTION; PRIORITY JOURNAL; PSEUDOGENE; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; REVIEW;

EID: 2942521197     PISSN: 0959440X     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.sbi.2004.05.007     Document Type: Review
Times cited : (99)

References (66)
  • 1
    • 0031586003 scopus 로고    scopus 로고
    • Prediction of complete gene structures in human genomic DNA
    • Burge C., Karlin S. Prediction of complete gene structures in human genomic DNA. J Mol Biol. 268:1997;78-94
    • (1997) J Mol Biol , vol.268 , pp. 78-94
    • Burge, C.1    Karlin, S.2
  • 3
    • 0030623944 scopus 로고    scopus 로고
    • Two methods for improving performance of an HMM and their application for gene finding
    • Krogh A. Two methods for improving performance of an HMM and their application for gene finding. Proc Int Conf Intell Syst Mol Biol. 5:1997;179-186
    • (1997) Proc Int Conf Intell Syst Mol Biol , vol.5 , pp. 179-186
    • Krogh, A.1
  • 5
    • 0034065724 scopus 로고    scopus 로고
    • Ab initio gene finding in Drosophila genomic DNA
    • Salamov A.A., Solovyev V.V. Ab initio gene finding in Drosophila genomic DNA. Genome Res. 10:2000;516-522
    • (2000) Genome Res , vol.10 , pp. 516-522
    • Salamov, A.A.1    Solovyev, V.V.2
  • 6
    • 0037268583 scopus 로고    scopus 로고
    • Comparative gene prediction in human and mouse
    • This paper describes the program SGP-2, and its application to the comparative analysis of the human and mouse genomes. SGP-2 is an extension of the GENEID program that incorporates genome alignments obtained with TBLASTX. The paper describes the details of the implementation and a number of factors that influence performance.
    • Parra G., Agarwal P., Abril J.F., Wiehe T., Fickett J.W., Guigo R. Comparative gene prediction in human and mouse. Genome Res. 13:2003;108-117 This paper describes the program SGP-2, and its application to the comparative analysis of the human and mouse genomes. SGP-2 is an extension of the GENEID program that incorporates genome alignments obtained with TBLASTX. The paper describes the details of the implementation and a number of factors that influence performance.
    • (2003) Genome Res , vol.13 , pp. 108-117
    • Parra, G.1    Agarwal, P.2    Abril, J.F.3    Wiehe, T.4    Fickett, J.W.5    Guigo, R.6
  • 7
    • 0037350957 scopus 로고    scopus 로고
    • SLAM: Cross-species gene finding and alignment with a generalized pair hidden Markov model
    • This paper introduces the generalized pair HMM, a hybrid of generalized HMMs for gene prediction and pair HMMs for sequence alignment, and describes its implementation in the SLAM program. In SLAM, the gene prediction and the sequence alignment are obtained simultaneously. SLAM, together with SGP-2 and TWINSCAN, was used in the comparative analysis of the human and mouse genomes.
    • Alexandersson M., Cawley S., Pachter L. SLAM: cross-species gene finding and alignment with a generalized pair hidden Markov model. Genome Res. 13:2003;496-502 This paper introduces the generalized pair HMM, a hybrid of generalized HMMs for gene prediction and pair HMMs for sequence alignment, and describes its implementation in the SLAM program. In SLAM, the gene prediction and the sequence alignment are obtained simultaneously. SLAM, together with SGP-2 and TWINSCAN, was used in the comparative analysis of the human and mouse genomes.
    • (2003) Genome Res , vol.13 , pp. 496-502
    • Alexandersson, M.1    Cawley, S.2    Pachter, L.3
  • 8
    • 17444437765 scopus 로고    scopus 로고
    • Integrating genomic homology into gene structure prediction
    • Korf I., Flicek P., Duan D., Brent M.R. Integrating genomic homology into gene structure prediction. Bioinformatics. 17(suppl 1):2001;S140-S148
    • (2001) Bioinformatics , vol.17 , Issue.SUPPL. 1 , pp. 140-S148
    • Korf, I.1    Flicek, P.2    Duan, D.3    Brent, M.R.4
  • 9
    • 0037264654 scopus 로고    scopus 로고
    • Leveraging the mouse genome for gene prediction in human: From whole-genome shotgun reads to a global synteny map
    • This paper describes how the program TWINSCAN was used to annotate the entire human genome, using alignments from the entire mouse genome. This was one of the most specific de novo annotations of the human genome ever, predicting about 60% as many exons and genes as GENSCAN while achieving a slighter higher sensitivity to known exons and genes. The paper includes a detailed analysis of TWINSCAN's accuracy and the factors that influence it, such as the number of available shotgun reads from the informant genome.
    • Flicek P., Keibler E., Hu P., Korf I., Brent M.R. Leveraging the mouse genome for gene prediction in human: from whole-genome shotgun reads to a global synteny map. Genome Res. 13:2003;46-54 This paper describes how the program TWINSCAN was used to annotate the entire human genome, using alignments from the entire mouse genome. This was one of the most specific de novo annotations of the human genome ever, predicting about 60% as many exons and genes as GENSCAN while achieving a slighter higher sensitivity to known exons and genes. The paper includes a detailed analysis of TWINSCAN's accuracy and the factors that influence it, such as the number of available shotgun reads from the informant genome.
    • (2003) Genome Res , vol.13 , pp. 46-54
    • Flicek, P.1    Keibler, E.2    Hu, P.3    Korf, I.4    Brent, M.R.5
  • 11
    • 0037311782 scopus 로고    scopus 로고
    • Gene finding with a hidden Markov model of genome structure and evolution
    • Pedersen J.S., Hein J. Gene finding with a hidden Markov model of genome structure and evolution. Bioinformatics. 19:2003;219-227
    • (2003) Bioinformatics , vol.19 , pp. 219-227
    • Pedersen, J.S.1    Hein, J.2
  • 12
    • 0346505461 scopus 로고    scopus 로고
    • Computational gene prediction using multiple sources of evidence
    • Allen J.E., Pertea M., Salzberg S.L. Computational gene prediction using multiple sources of evidence. Genome Res. 14:2004;142-148
    • (2004) Genome Res , vol.14 , pp. 142-148
    • Allen, J.E.1    Pertea, M.2    Salzberg, S.L.3
  • 14
    • 0037417884 scopus 로고    scopus 로고
    • Comparison of mouse and human genomes followed by experimental verification yields an estimated 1,019 additional genes
    • This paper describes a computational pipeline that exploits the human and mouse genome sequences to produce a set of gene predictions with a very high rate of experimental verification by RT-PCR. The first stage of the pipeline is the analysis of the genome sequence with dual-genome predictors. The second stage of the pipeline is based on the observation that almost all mouse genes have a human counterpart with highly conserved exonic structure. Therefore, computational predictions are retained only if the protein predicted in mouse aligns with a predicted human protein with at least one predicted intron in the same location. Experimental verification rates for these predictions reached 76%.
    • Guigó R., Dermitzakis E.T., Agarwal P., Ponting C., Parra G., Reymond A., Abril J.F., Keibler E., Lyle R., Ucla C., et al. Comparison of mouse and human genomes followed by experimental verification yields an estimated 1, 019 additional genes. Proc Natl Acad Sci USA. 100:2003;1140-1145 This paper describes a computational pipeline that exploits the human and mouse genome sequences to produce a set of gene predictions with a very high rate of experimental verification by RT-PCR. The first stage of the pipeline is the analysis of the genome sequence with dual-genome predictors. The second stage of the pipeline is based on the observation that almost all mouse genes have a human counterpart with highly conserved exonic structure. Therefore, computational predictions are retained only if the protein predicted in mouse aligns with a predicted human protein with at least one predicted intron in the same location. Experimental verification rates for these predictions reached 76%.
    • (2003) Proc Natl Acad Sci USA , vol.100 , pp. 1140-1145
    • Guigó, R.1    Dermitzakis, E.T.2    Agarwal, P.3    Ponting, C.4    Parra, G.5    Reymond, A.6    Abril, J.F.7    Keibler, E.8    Lyle, R.9    Ucla, C.10
  • 15
    • 1842768392 scopus 로고    scopus 로고
    • Identification of rat genes by TWINSCAN gene prediction, RT-PCR, and direct sequencing
    • Wu J.Q., Shteynberg D., Arumugam M., Gibbs R.A., Brent M.R. Identification of rat genes by TWINSCAN gene prediction, RT-PCR, and direct sequencing. Genome Res. 14:2004;665-671
    • (2004) Genome Res , vol.14 , pp. 665-671
    • Wu, J.Q.1    Shteynberg, D.2    Arumugam, M.3    Gibbs, R.A.4    Brent, M.R.5
  • 16
    • 1842818736 scopus 로고    scopus 로고
    • Accurate identification of novel human genes through simultaneous gene prediction in human, mouse, and rat
    • Dewey C., Wu J.Q., Cawley S., Alexandersson M., Gibbs R., Pachter L. Accurate identification of novel human genes through simultaneous gene prediction in human, mouse, and rat. Genome Res. 14:2004;661-664
    • (2004) Genome Res , vol.14 , pp. 661-664
    • Dewey, C.1    Wu, J.Q.2    Cawley, S.3    Alexandersson, M.4    Gibbs, R.5    Pachter, L.6
  • 17
    • 0346752110 scopus 로고    scopus 로고
    • Millions of years of evolution preserved: A comprehensive catalog of the processed pseudogenes in the human genome
    • Zhang Z., Harrison P.M., Liu Y., Gerstein M. Millions of years of evolution preserved: a comprehensive catalog of the processed pseudogenes in the human genome. Genome Res. 13:2003;2541-2558
    • (2003) Genome Res , vol.13 , pp. 2541-2558
    • Zhang, Z.1    Harrison, P.M.2    Liu, Y.3    Gerstein, M.4
  • 18
  • 19
    • 2942542619 scopus 로고    scopus 로고
    • The status, quality and expansion of the NIH full-length cDNA project (MGC)
    • in press.
    • The MGC Project Team: The status, quality and expansion of the NIH full-length cDNA project (MGC). Genome Res 2004, 14:in press.
    • (2004) Genome Res , vol.14
  • 20
    • 0037803471 scopus 로고    scopus 로고
    • Human-mouse gene identification by comparative evidence integration and evolutionary analysis
    • This paper provides a detailed analysis of three important components of comparative gene predictors: the selection of the most appropriate reference genome; the selection of the most appropriate comparative features to be included in the gene prediction framework; and the selection of the architecture to integrate these comparative features.
    • Zhang L., Pavlovic V., Cantor C.R., Kasif S. Human-mouse gene identification by comparative evidence integration and evolutionary analysis. Genome Res. 13:2003;1190-1202 This paper provides a detailed analysis of three important components of comparative gene predictors: the selection of the most appropriate reference genome; the selection of the most appropriate comparative features to be included in the gene prediction framework; and the selection of the architecture to integrate these comparative features.
    • (2003) Genome Res , vol.13 , pp. 1190-1202
    • Zhang, L.1    Pavlovic, V.2    Cantor, C.R.3    Kasif, S.4
  • 21
    • 0042525755 scopus 로고    scopus 로고
    • Gene prediction by spectral rotation measure: A new method for identifying protein-coding regions
    • Kotlar D., Lavner Y. Gene prediction by spectral rotation measure: a new method for identifying protein-coding regions. Genome Res. 13:2003;1930-1937
    • (2003) Genome Res , vol.13 , pp. 1930-1937
    • Kotlar, D.1    Lavner, Y.2
  • 23
    • 0037866728 scopus 로고    scopus 로고
    • An evolutionary approach reveals a high protein-coding capacity of the human genome
    • Nekrutenko A., Chung W.Y., Li W.H. An evolutionary approach reveals a high protein-coding capacity of the human genome. Trends Genet. 19:2003;306-310
    • (2003) Trends Genet , vol.19 , pp. 306-310
    • Nekrutenko, A.1    Chung, W.Y.2    Li, W.H.3
  • 24
    • 0042622195 scopus 로고    scopus 로고
    • ETOPE: Evolutionary test of predicted exons
    • Nekrutenko A., Chung W.Y., Li W.H. ETOPE: evolutionary test of predicted exons. Nucleic Acids Res. 31:2003;3564-3567
    • (2003) Nucleic Acids Res , vol.31 , pp. 3564-3567
    • Nekrutenko, A.1    Chung, W.Y.2    Li, W.H.3
  • 25
    • 0346888663 scopus 로고    scopus 로고
    • Gene structure prediction in syntenic DNA segments
    • Moore J.E., Lake J.A. Gene structure prediction in syntenic DNA segments. Nucleic Acids Res. 31:2003;7271-7279
    • (2003) Nucleic Acids Res , vol.31 , pp. 7271-7279
    • Moore, J.E.1    Lake, J.A.2
  • 26
    • 0642374379 scopus 로고    scopus 로고
    • A novel index which precisely derives protein coding regions from cross-species genome alignments
    • Noguchi H., Yada T., Sakaki Y. A novel index which precisely derives protein coding regions from cross-species genome alignments. Genome Inform Ser Workshop Genome Inform. 13:2002;183-191
    • (2002) Genome Inform Ser Workshop Genome Inform , vol.13 , pp. 183-191
    • Noguchi, H.1    Yada, T.2    Sakaki, Y.3
  • 28
    • 2942519269 scopus 로고    scopus 로고
    • Gene prediction accuracy in large DNA sequences
    • Edited by Koonin EV, Galperin MY. Norfolk, UK: Caister Academic Press
    • Guigó R, Wiehe T: Gene prediction accuracy in large DNA sequences. In Frontiers in Computational Genomics. Edited by Koonin EV, Galperin MY. Norfolk, UK: Caister Academic Press; 2003:1-33. [Saier MH Jr (Series Editor): Functional Genomics Series, vol 3.]
    • (2003) Frontiers in Computational Genomics , pp. 1-33
    • Guigó, R.1    Wiehe, T.2
  • 29
    • 2942577442 scopus 로고    scopus 로고
    • Guigó R, Wiehe T: Gene prediction accuracy in large DNA sequences. In Frontiers in Computational Genomics. Edited by Koonin EV, Galperin MY. Norfolk, UK: Caister Academic Press; 2003:1-33. [Saier MH Jr (Series Editor): Functional Genomics Series, vol 3.]
    • Functional Genomics Series , vol.3
    • Saier Jr., M.H.1
  • 30
    • 2942541121 scopus 로고    scopus 로고
    • The effects of evolutionary distance on TWINSCAN, an algorithm for pairwise comparative gene prediction
    • Edited by Stillman B, Stewart D. Cold Spring Harbor, NY, USA: Cold Spring Harbor Laboratory Press
    • Wang M, Buhler J, Brent MR: The effects of evolutionary distance on TWINSCAN, an algorithm for pairwise comparative gene prediction. In The Genome of Homo Sapiens. Edited by Stillman B, Stewart D. Cold Spring Harbor, NY, USA: Cold Spring Harbor Laboratory Press; 2004:125-130.
    • (2004) The Genome of Homo Sapiens , pp. 125-130
    • Wang, M.1    Buhler, J.2    Brent, M.R.3
  • 32
    • 0034791551 scopus 로고    scopus 로고
    • Evolutionary HMMs: A Bayesian approach to multiple alignment
    • Holmes I., Bruno W.J. Evolutionary HMMs: a Bayesian approach to multiple alignment. Bioinformatics. 17:2001;803-820
    • (2001) Bioinformatics , vol.17 , pp. 803-820
    • Holmes, I.1    Bruno, W.J.2
  • 35
    • 0034098730 scopus 로고    scopus 로고
    • Using GeneWise in the Drosophila annotation experiment
    • Birney E., Durbin R. Using GeneWise in the Drosophila annotation experiment. Genome Res. 10:2000;547-548
    • (2000) Genome Res , vol.10 , pp. 547-548
    • Birney, E.1    Durbin, R.2
  • 36
    • 0036708637 scopus 로고    scopus 로고
    • GAZE: A generic framework for the integration of gene-prediction data by dynamic programming
    • Howe K.L., Chothia T., Durbin R. GAZE: a generic framework for the integration of gene-prediction data by dynamic programming. Genome Res. 12:2002;1418-1427
    • (2002) Genome Res , vol.12 , pp. 1418-1427
    • Howe, K.L.1    Chothia, T.2    Durbin, R.3
  • 37
    • 0036173326 scopus 로고    scopus 로고
    • A Bayesian framework for combining gene predictions
    • Pavlovic V., Garg A., Kasif S. A Bayesian framework for combining gene predictions. Bioinformatics. 18:2002;19-27
    • (2002) Bioinformatics , vol.18 , pp. 19-27
    • Pavlovic, V.1    Garg, A.2    Kasif, S.3
  • 38
    • 0038479970 scopus 로고    scopus 로고
    • Computational discovery of internal micro-exons
    • Volfovsky N., Haas B.J., Salzberg S.L. Computational discovery of internal micro-exons. Genome Res. 13:2003;1216-1221
    • (2003) Genome Res , vol.13 , pp. 1216-1221
    • Volfovsky, N.1    Haas, B.J.2    Salzberg, S.L.3
  • 39
    • 1342263801 scopus 로고    scopus 로고
    • Gene structure conservation aids similarity based gene prediction
    • Meyer I.M., Durbin R. Gene structure conservation aids similarity based gene prediction. Nucleic Acids Res. 32:2004;776-783
    • (2004) Nucleic Acids Res , vol.32 , pp. 776-783
    • Meyer, I.M.1    Durbin, R.2
  • 40
    • 2442690356 scopus 로고    scopus 로고
    • Gene structure prediction from consensus spliced alignment of multiple ESTs matching the same genomic locus
    • in press.
    • Brendel V, Xing L, Zhu W: Gene structure prediction from consensus spliced alignment of multiple ESTs matching the same genomic locus. Bioinformatics 2004, in press.
    • (2004) Bioinformatics
    • Brendel, V.1    Xing, L.2    Zhu, W.3
  • 41
    • 0030878280 scopus 로고    scopus 로고
    • A branch point consensus from Arabidopsis found by non-circular analysis allows for better prediction of acceptor sites
    • Tolstrup N., Rouze P., Brunak S. A branch point consensus from Arabidopsis found by non-circular analysis allows for better prediction of acceptor sites. Nucleic Acids Res. 25:1997;3159-3163
    • (1997) Nucleic Acids Res , vol.25 , pp. 3159-3163
    • Tolstrup, N.1    Rouze, P.2    Brunak, S.3
  • 42
    • 0344874227 scopus 로고    scopus 로고
    • Splice site prediction with quadratic discriminant analysis using diversity measure
    • Zhang L., Luo L. Splice site prediction with quadratic discriminant analysis using diversity measure. Nucleic Acids Res. 31:2003;6214-6220
    • (2003) Nucleic Acids Res , vol.31 , pp. 6214-6220
    • Zhang, L.1    Luo, L.2
  • 43
    • 0346121460 scopus 로고    scopus 로고
    • Sequence information for the splicing of human pre-mRNA identified by support vector machine classification
    • This paper describes an analysis of sequence patterns found in intronic regions upstream of splice acceptors and downstream of splice donors. Current gene prediction programs predict splice site locations using only the regions relatively near to a potential splice site, but this paper suggests that gene prediction may be improved by extending splicing models further into the intron.
    • Zhang X.H., Heller K.A., Hefter I., Leslie C.S., Chasin L.A. Sequence information for the splicing of human pre-mRNA identified by support vector machine classification. Genome Res. 13:2003;2637-2650 This paper describes an analysis of sequence patterns found in intronic regions upstream of splice acceptors and downstream of splice donors. Current gene prediction programs predict splice site locations using only the regions relatively near to a potential splice site, but this paper suggests that gene prediction may be improved by extending splicing models further into the intron.
    • (2003) Genome Res , vol.13 , pp. 2637-2650
    • Zhang, X.H.1    Heller, K.A.2    Hefter, I.3    Leslie, C.S.4    Chasin, L.A.5
  • 44
    • 2942594395 scopus 로고    scopus 로고
    • Fast feature selection using a simple estimation of distribution algorithm: A case study on splice site prediction
    • Saeys Y., Degroeve S., Aeyels D., Van De Peer Y., Rouze P. Fast feature selection using a simple estimation of distribution algorithm: a case study on splice site prediction. Bioinformatics. 19(suppl 2):2003;II179-II188
    • (2003) Bioinformatics , vol.19 , Issue.SUPPL. 2 , pp. 179-II188
    • Saeys, Y.1    Degroeve, S.2    Aeyels, D.3    Van De Peer, Y.4    Rouze, P.5
  • 46
    • 0344289654 scopus 로고    scopus 로고
    • Modeling splicing sites with pairwise correlations
    • Arita M., Tsuda K., Asai K. Modeling splicing sites with pairwise correlations. Bioinformatics. 18(suppl 2):2002;S27-S34
    • (2002) Bioinformatics , vol.18 , Issue.SUPPL. 2 , pp. 27-S34
    • Arita, M.1    Tsuda, K.2    Asai, K.3
  • 47
    • 2942520939 scopus 로고    scopus 로고
    • Splice site identification by idlBNs
    • in press.
    • Castelo R, Guigo R: Splice site identification by idlBNs. Bioinformatics 2004, in press.
    • (2004) Bioinformatics
    • Castelo, R.1    Guigo, R.2
  • 48
    • 0036911605 scopus 로고    scopus 로고
    • Distribution and characterization of regulatory elements in the human genome
    • Majewski J., Ott J. Distribution and characterization of regulatory elements in the human genome. Genome Res. 12:2002;1827-1836
    • (2002) Genome Res , vol.12 , pp. 1827-1836
    • Majewski, J.1    Ott, J.2
  • 49
    • 0037047644 scopus 로고    scopus 로고
    • Predictive identification of exonic splicing enhancers in human genes
    • This paper describes a statistical analysis of over-represented oligonucleotides in the sequence of exons with weak splice signals. The analysis led to the identification of ten exonic splicing enhancers, which were subsequently found to display enhancer activity in vivo.
    • Fairbrother W.G., Yeh R.F., Sharp P.A., Burge C.B. Predictive identification of exonic splicing enhancers in human genes. Science. 297:2002;1007-1013 This paper describes a statistical analysis of over-represented oligonucleotides in the sequence of exons with weak splice signals. The analysis led to the identification of ten exonic splicing enhancers, which were subsequently found to display enhancer activity in vivo.
    • (2002) Science , vol.297 , pp. 1007-1013
    • Fairbrother, W.G.1    Yeh, R.F.2    Sharp, P.A.3    Burge, C.B.4
  • 50
    • 0346505472 scopus 로고    scopus 로고
    • Ordered partitioning reveals extended splice-site consensus information
    • This paper reports that long introns have stronger splice site consensus signals than short introns. Incorporating this relationship into gene prediction models may help to overcome the difficulty in predicting long introns, particularly in combination with better models of the intron length distribution itself.
    • Weir M., Rice M. Ordered partitioning reveals extended splice-site consensus information. Genome Res. 14:2004;67-78 This paper reports that long introns have stronger splice site consensus signals than short introns. Incorporating this relationship into gene prediction models may help to overcome the difficulty in predicting long introns, particularly in combination with better models of the intron length distribution itself.
    • (2004) Genome Res , vol.14 , pp. 67-78
    • Weir, M.1    Rice, M.2
  • 51
    • 0035949674 scopus 로고    scopus 로고
    • A computational analysis of sequence features involved in recognition of short introns
    • Lim L.P., Burge C.B. A computational analysis of sequence features involved in recognition of short introns. Proc Natl Acad Sci USA. 98:2001;11193-11198
    • (2001) Proc Natl Acad Sci USA , vol.98 , pp. 11193-11198
    • Lim, L.P.1    Burge, C.B.2
  • 53
    • 2942527473 scopus 로고    scopus 로고
    • Gene prediction with a hidden Markov model and a new intron submodel
    • This paper describes a single-genome de novo gene prediction program that is based on an HMM model with number of elegant features that have not been previously described. The most significant is a new compromise between speed and accuracy that allows relatively accurate modeling of the distribution of intron lengths to be used without imposing an unacceptably long running time.
    • Stanke M., Waack S. Gene prediction with a hidden Markov model and a new intron submodel. Bioinformatics. 19(suppl 2):2003;II215-II225 This paper describes a single-genome de novo gene prediction program that is based on an HMM model with number of elegant features that have not been previously described. The most significant is a new compromise between speed and accuracy that allows relatively accurate modeling of the distribution of intron lengths to be used without imposing an unacceptably long running time.
    • (2003) Bioinformatics , vol.19 , Issue.SUPPL. 2 , pp. 215-II225
    • Stanke, M.1    Waack, S.2
  • 57
    • 0036081146 scopus 로고    scopus 로고
    • DBTSS: Database of human transcriptional start sites and full-length cDNAs
    • Suzuki Y., Yamashita R., Nakai K., Sugano S. DBTSS: database of human transcriptional start sites and full-length cDNAs. Nucleic Acids Res. 30:2002;328-331
    • (2002) Nucleic Acids Res , vol.30 , pp. 328-331
    • Suzuki, Y.1    Yamashita, R.2    Nakai, K.3    Sugano, S.4
  • 58
    • 0042525750 scopus 로고    scopus 로고
    • Dragon gene start finder: An advanced system for finding approximate locations of the start of gene transcriptional units
    • Bajic V.B., Seah S.H. Dragon gene start finder: an advanced system for finding approximate locations of the start of gene transcriptional units. Genome Res. 13:2003;1923-1929
    • (2003) Genome Res , vol.13 , pp. 1923-1929
    • Bajic, V.B.1    Seah, S.H.2
  • 59
    • 1842584947 scopus 로고    scopus 로고
    • Applied bioinformatics for the identification of regulatory elements
    • Wasserman W.W., Sandelin A. Applied bioinformatics for the identification of regulatory elements. Nat Rev Genet. 5:2004;276-287
    • (2004) Nat Rev Genet , vol.5 , pp. 276-287
    • Wasserman, W.W.1    Sandelin, A.2
  • 60
    • 2442700175 scopus 로고    scopus 로고
    • ESTGenes: Alternative splicing from ESTs in Ensembl
    • in press.
    • Eyras E, Caccamo M, Curwen V, Clamp M: ESTGenes: alternative splicing from ESTs in Ensembl. Genome Res 2004, in press.
    • (2004) Genome Res
    • Eyras, E.1    Caccamo, M.2    Curwen, V.3    Clamp, M.4
  • 61
    • 0037705467 scopus 로고    scopus 로고
    • Conservation of human alternative splice events in mouse
    • Thanaraj T.A., Clark F., Muilu J. Conservation of human alternative splice events in mouse. Nucleic Acids Res. 31:2003;1-9
    • (2003) Nucleic Acids Res , vol.31 , pp. 1-9
    • Thanaraj, T.A.1    Clark, F.2    Muilu, J.3
  • 63
    • 2942610553 scopus 로고    scopus 로고
    • HMM sampling and applications to gene finding and alternative splicing
    • Cawley S.L., Pachter L. HMM sampling and applications to gene finding and alternative splicing. Bioinformatics. 19(suppl 2):2003;II36-II41
    • (2003) Bioinformatics , vol.19 , Issue.SUPPL. 2 , pp. 36-II41
    • Cawley, S.L.1    Pachter, L.2
  • 65
    • 1242321034 scopus 로고    scopus 로고
    • Reconsidering the evolution of eukaryotic selenoproteins: A novel nonmammalian family with scattered phylogenetic distribution
    • Castellano S., Novoselov S.V., Kryukov G.V., Lescure A., Blanco E., Krol A., Gladyshev V.N., Guigo R. Reconsidering the evolution of eukaryotic selenoproteins: a novel nonmammalian family with scattered phylogenetic distribution. EMBO Rep. 5:2004;71-77
    • (2004) EMBO Rep , vol.5 , pp. 71-77
    • Castellano, S.1    Novoselov, S.V.2    Kryukov, G.V.3    Lescure, A.4    Blanco, E.5    Krol, A.6    Gladyshev, V.N.7    Guigo, R.8
  • 66
    • 0001468848 scopus 로고    scopus 로고
    • Splicing precursors to mRNAs by the spliceosomes
    • Edited by Gesteland RF, Cech TR, Atkins J. Cold Spring Harbor, New York: Cold Spring Harbor Laboratory Press; chapter 20.
    • Burge CB, Tuschl T, Sharp PS: Splicing precursors to mRNAs by the spliceosomes. In The RNA World. Edited by Gesteland RF, Cech TR, Atkins J. Cold Spring Harbor, New York: Cold Spring Harbor Laboratory Press; 1999:chapter 20.
    • (1999) The RNA World
    • Burge, C.B.1    Tuschl, T.2    Sharp, P.S.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.