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Volumn 3, Issue 2, 2008, Pages 87-97

Genome annotation in plants and fungi: EuGène as a model platform

Author keywords

Fungi; Gene finding; Genome annotation; Plants

Indexed keywords


EID: 66249109710     PISSN: 15748936     EISSN: None     Source Type: Journal    
DOI: 10.2174/157489308784340702     Document Type: Article
Times cited : (76)

References (48)
  • 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 1997; 268: 78-94.
    • (1997) J Mol Biol , vol.268 , pp. 78-94
    • Burge, C.1    Karlin, S.2
  • 2
    • 0024610919 scopus 로고
    • A tutorial on hidden Markov models and selected applications in speech recognition
    • Rabiner L. A tutorial on hidden Markov models and selected applications in speech recognition. Proceedings of the IEEE 1989; 77: 257-286.
    • (1989) Proceedings of the IEEE , vol.77 , pp. 257-286
    • Rabiner, L.1
  • 3
    • 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; 17 Suppl 1: p. S140-148.
    • (2001) Bioinformatics , vol.17 , Issue.SUPPL. 1
    • Korf, I.1    Flicek, P.2    Duan, D.3    Brent, M.R.4
  • 4
    • 19844374535 scopus 로고    scopus 로고
    • Begin at the beginning: Predicting genes with 5' UTRs
    • Brown RH, Gross SS, Brent MR. Begin at the beginning: predicting genes with 5' UTRs. Genome Res 2005; 15: 742-747.
    • (2005) Genome Res , vol.15 , pp. 742-747
    • Brown, R.H.1    Gross, S.S.2    Brent, M.R.3
  • 6
    • 24644485994 scopus 로고    scopus 로고
    • Jigsaw: Integration of multiple sources of evidence for gene prediction
    • Allen JE, Salzberg SL. Jigsaw: integration of multiple sources of evidence for gene prediction. Bioinformatics 2005; 21: 3596-3603.
    • (2005) Bioinformatics , vol.21 , pp. 3596-3603
    • Allen, J.E.1    Salzberg, S.L.2
  • 7
    • 84959057192 scopus 로고    scopus 로고
    • EuGène: An eucaryotic gene finder that combines several sources of evidence
    • Schiex T, Moisan A, Rouzé P. EuGène: an eucaryotic gene finder that combines several sources of evidence. Lect Notes Comput Sci 2001; 2066: 111-125.
    • (2066) Lect Notes Comput Sci , vol.2001 , pp. 111-125
    • Schiex, T.1    Moisan, A.2    Rouzé, P.3
  • 9
    • 0027377256 scopus 로고
    • A weight array method for splicing signal analysis
    • Zhang MQ, Marr TG. A weight array method for splicing signal analysis. Comput Appl Biosci 1993; 9: 499-509.
    • (1993) Comput Appl Biosci , vol.9 , pp. 499-509
    • Zhang, M.Q.1    Marr, T.G.2
  • 10
    • 17444380495 scopus 로고    scopus 로고
    • Splicemachine: Predicting splice sites from high-dimensional local context representations
    • Degroeve S, Saeys Y, De Baets B, Rouzé P, Van De Peer Y. Splicemachine: predicting splice sites from high-dimensional local context representations. Bioinformatics 2005, 21: 1332-1338.
    • (2005) Bioinformatics , vol.21 , pp. 1332-1338
    • Degroeve, S.1    Saeys, Y.2    De Baets, B.3    Rouzé, P.4    Van De Peer, Y.5
  • 11
    • 0042121130 scopus 로고    scopus 로고
    • Geneseqer at plantgdb: Gene structure prediction in plant genomes
    • Schlueter SD, Dong Q, Brendel V. Geneseqer at plantgdb: gene structure prediction in plant genomes. Nucleic Acids Res 2003; 31: 3597-3600.
    • (2003) Nucleic Acids Res , vol.31 , pp. 3597-3600
    • Schlueter, S.D.1    Dong, Q.2    Brendel, V.3
  • 12
    • 28844465123 scopus 로고    scopus 로고
    • Engineering a software tool for gene structure prediction in higher organisms
    • Gremme G, Brendel V, Sparks M, Kurtz S. Engineering a software tool for gene structure prediction in higher organisms. Inf Softw Technol 2005; 47: 965-978.
    • (2005) Inf Softw Technol , vol.47 , pp. 965-978
    • Gremme, G.1    Brendel, V.2    Sparks, M.3    Kurtz, S.4
  • 13
    • 0035002015 scopus 로고    scopus 로고
    • Computational inference of homologous gene structures in the human genome
    • Yeh RF, Lim LP, Burge CB. Computational inference of homologous gene structures in the human genome. Genome Res 2001; 11: 803-816.
    • (2001) Genome Res , vol.11 , pp. 803-816
    • Yeh, R.F.1    Lim, L.P.2    Burge, C.B.3
  • 14
    • 33645979674 scopus 로고    scopus 로고
    • Using multiple alignments to improve gene prediction
    • Gross SS, Brent MR. Using multiple alignments to improve gene prediction. J Comput Biol 2006 13: 379-393.
    • (2006) J Comput Biol , vol.13 , pp. 379-393
    • Gross, S.S.1    Brent, M.R.2
  • 15
    • 0037350957 scopus 로고    scopus 로고
    • Slam: Cross-species gene finding and alignment with a generalized pair hidden Markov model
    • Alexandersson M, Cawley S, Pachter L. Slam: cross-species gene finding and alignment with a generalized pair hidden Markov model. Genome Res 2003; 13: 496-502.
    • (2003) Genome Res , vol.13 , pp. 496-502
    • Alexandersson, M.1    Cawley, S.2    Pachter, L.3
  • 16
    • 84898962087 scopus 로고    scopus 로고
    • Semi-Markov conditional random fields for information extraction
    • In: Saul LK, Weiss Y, Bottou Y Eds, Vancouver, BC, Canada
    • th Neural Information Processing Systems (NIPS), Vancouver, BC, Canada, 2005; 17: 1185-1192 [http//books.nips.cc/nips17.-html]
    • (2005) th Neural Information Processing Systems (NIPS) , vol.17 , pp. 1185-1192
    • Sarawagi, S.1    Cohen, W.2
  • 19
    • 33846942242 scopus 로고    scopus 로고
    • Experimental validation of novel genes predicted in the un-annotated regions of the arabidopsis genome
    • Moskal WAJ, Wu HC, Underwood BA, Wang W, Town CD, Xiao Y. Experimental validation of novel genes predicted in the un-annotated regions of the arabidopsis genome. BMC Genomics 2007; 8: 18.
    • (2007) BMC Genomics , vol.8 , pp. 18
    • Moskal, W.A.J.1    Wu, H.C.2    Underwood, B.A.3    Wang, W.4    Town, C.D.5    Xiao, Y.6
  • 20
    • 38849191929 scopus 로고    scopus 로고
    • Analysis of CATMA transcriptome data identifies hundreds of novel functional genes and improves gene models in the Arabidopsis genome
    • Aubourg S, Martin-Vigniette ML, Brunaud V, et al. Analysis of CATMA transcriptome data identifies hundreds of novel functional genes and improves gene models in the Arabidopsis genome. BMC Genomics 2007; 8: 401.
    • (2007) BMC Genomics , vol.8 , pp. 401
    • Aubourg, S.1    Martin-Vigniette, M.L.2    Brunaud, V.3
  • 21
    • 0041589538 scopus 로고    scopus 로고
    • EuGene'Hom: A generic similarity-based gene finder using multiple homologous sequences
    • Foissac S, Bardou P, Moisan A, Cros M, Schiex T. EuGene'Hom: a generic similarity-based gene finder using multiple homologous sequences. Nucleic Acids Res 2003; 31: 3742-3745.
    • (2003) Nucleic Acids Res , vol.31 , pp. 3742-3745
    • Foissac, S.1    Bardou, P.2    Moisan, A.3    Cros, M.4    Schiex, T.5
  • 22
    • 25444512373 scopus 로고    scopus 로고
    • Integrating alternative splicing detection into gene prediction
    • Foissac S, Schiex T. Integrating alternative splicing detection into gene prediction. BMC Bioinformatics 2005; 6: 25.
    • (2005) BMC Bioinformatics , vol.6 , pp. 25
    • Foissac, S.1    Schiex, T.2
  • 23
  • 24
    • 0036708637 scopus 로고    scopus 로고
    • Gaze: A generic framework for the integration of gene-prediction data by dynamic programming
    • Howe KL, Chothia T, Durbin R. Gaze: a generic framework for the integration of gene-prediction data by dynamic programming. Genome Res 2002; 12: 1418-1427.
    • (2002) Genome Res , vol.12 , pp. 1418-1427
    • Howe, K.L.1    Chothia, T.2    Durbin, R.3
  • 25
    • 33645161645 scopus 로고    scopus 로고
    • Gene prediction in eukaryotes with a generalized hidden Markov model that uses hints from external sources
    • Stanke M, Schöffmann O, Morgenstern B, Waack S. Gene prediction in eukaryotes with a generalized hidden Markov model that uses hints from external sources. BMC Bioinformatics 2006; 7: 62.
    • (2006) BMC Bioinformatics , vol.7 , pp. 62
    • Stanke, M.1    Schöffmann, O.2    Morgenstern, B.3    Waack, S.4
  • 26
    • 13244268374 scopus 로고    scopus 로고
    • An empirical analysis of training protocols for probabilistic gene finders
    • Majoros WH, Salzberg SL. An empirical analysis of training protocols for probabilistic gene finders. BMC Bioinformatics 2004; 5: 206.
    • (2004) BMC Bioinformatics , vol.5 , pp. 206
    • Majoros, W.H.1    Salzberg, S.L.2
  • 27
    • 33748641488 scopus 로고    scopus 로고
    • Jigsaw, Genezilla, and GlimmerHMM: Puzzling out the features of human genes in the encode regions
    • Allen JE, Majoros WH, Pertea M, Salzberg SL. Jigsaw, Genezilla, and GlimmerHMM: puzzling out the features of human genes in the encode regions. Genome Biol 2006; 7 Suppl 1: S9.1-13.
    • (2006) Genome Biol , vol.7 , Issue.SUPPL. 1 , pp. 1-13
    • Allen, J.E.1    Majoros, W.H.2    Pertea, M.3    Salzberg, S.L.4
  • 28
    • 33748674197 scopus 로고    scopus 로고
    • Augustus at EGasp: Using EST, protein and genomic alignments for improved gene prediction in the human genome
    • Stanke M, Tzvetkova A, Morgenstern B. Augustus at EGasp: using EST, protein and genomic alignments for improved gene prediction in the human genome. Genome Biol 2006; 7 Suppl 1: S11-18.
    • (2006) Genome Biol , vol.7 , Issue.SUPPL. 1
    • Stanke, M.1    Tzvetkova, A.2    Morgenstern, B.3
  • 29
    • 33750489449 scopus 로고    scopus 로고
    • Statistical inference of chromosomal homology based on gene colinear-ity and applications to Arabidopsis and rice
    • Wang X, Shi X, Li Z, Zhu Q, Kong L, Tang W, Ge S, Luo J. Statistical inference of chromosomal homology based on gene colinear-ity and applications to Arabidopsis and rice. BMC Bioinformatics 2006; 7: 447.
    • (2006) BMC Bioinformatics , vol.7 , pp. 447
    • Wang, X.1    Shi, X.2    Li, Z.3    Zhu, Q.4    Kong, L.5    Tang, W.6    Ge, S.7    Luo, J.8
  • 30
    • 0030627982 scopus 로고    scopus 로고
    • Neural network prediction of translation initiation sites in eukaryotes: Perspectives for EST and genome analysis
    • Pedersen AG, Nielsen H. Neural network prediction of translation initiation sites in eukaryotes: perspectives for EST and genome analysis. Proc Int Conf Intell Syst Mol Biol 1997; 5: 226-233.
    • (1997) Proc Int Conf Intell Syst Mol Biol , vol.5 , pp. 226-233
    • Pedersen, A.G.1    Nielsen, H.2
  • 31
    • 0029791403 scopus 로고    scopus 로고
    • Splice site prediction in Arabidopsis thaliana pre-mRNA by combining local and global sequence information
    • Hebsgaard SM, Korning PG, Tolstrup N, et al. Splice site prediction in Arabidopsis thaliana pre-mRNA by combining local and global sequence information. Nucleic Acids Res 1996; 24: 3439-3452.
    • (1996) Nucleic Acids Res , vol.24 , pp. 3439-3452
    • Hebsgaard, S.M.1    Korning, P.G.2    Tolstrup, N.3
  • 32
    • 0029822410 scopus 로고    scopus 로고
    • Logitlinear models for the prediction of splice sites in plant pre-mRNA sequences
    • Kleffe J, Hermann K, Vahrson W, Wittig B, Brendel V. Logitlinear models for the prediction of splice sites in plant pre-mRNA sequences. Nucleic Acids Res 1996; 24: 4709-4718.
    • (1996) Nucleic Acids Res , vol.24 , pp. 4709-4718
    • Kleffe, J.1    Hermann, K.2    Vahrson, W.3    Wittig, B.4    Brendel, V.5
  • 34
    • 0033381623 scopus 로고    scopus 로고
    • Evaluation of gene prediction software using a genomic data set: Application to Arabidopsis thaliana sequences
    • Pavy N, Rombauts S, Déhais P, et al. Evaluation of gene prediction software using a genomic data set: application to Arabidopsis thaliana sequences. Bioinformatics 1999; 15: 887-899.
    • (1999) Bioinformatics , vol.15 , pp. 887-899
    • Pavy, N.1    Rombauts, S.2    Déhais, P.3
  • 36
    • 0031732094 scopus 로고    scopus 로고
    • A computer program for aligning a cDNA sequence with a genomic DNA sequence
    • Florea L, Hartzell G, Zhang Z, Rubin GM, Miller W. A computer program for aligning a cDNA sequence with a genomic DNA sequence. Genome Res 1998; 8: 967-974.
    • (1998) Genome Res , vol.8 , pp. 967-974
    • Florea, L.1    Hartzell, G.2    Zhang, Z.3    Rubin, G.M.4    Miller, W.5
  • 37
    • 0030801002 scopus 로고    scopus 로고
    • Gapped BLAST and PSI-BLAST: A new generation of protein database search programs
    • Altschul SF, Madden TL, Schäffer AA, et al. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 1997; 25: 3389-3402.
    • (1997) Nucleic Acids Res , vol.25 , pp. 3389-3402
    • Altschul, S.F.1    Madden, T.L.2    Schäffer, A.A.3
  • 38
    • 0037252603 scopus 로고    scopus 로고
    • CATMA: A complete Arabidopsis GST database
    • Crowe ML, Serizet C, Thareau V, et al. CATMA: a complete Arabidopsis GST database. Nucleic Acids Res 2003; 31: 156-158.
    • (2003) Nucleic Acids Res , vol.31 , pp. 156-158
    • Crowe, M.L.1    Serizet, C.2    Thareau, V.3
  • 40
    • 20244377471 scopus 로고    scopus 로고
    • Functional annotation of a full-length Arabidopsis cDNA collection
    • Seki M, Narusaka M, Kamiya A, et al. Functional annotation of a full-length Arabidopsis cDNA collection. Science 2002; 296: 141-145.
    • (2002) Science , vol.296 , pp. 141-145
    • Seki, M.1    Narusaka, M.2    Kamiya, A.3
  • 41
    • 0037115831 scopus 로고    scopus 로고
    • Exploring root symbiotic programs in the model legume Medicago truncatula using EST analysis
    • Journet E, van Tuinen D, Gouzy J, et al. Exploring root symbiotic programs in the model legume Medicago truncatula using EST analysis. Nucleic Acids Res 2002; 30: 5579-5592.
    • (2002) Nucleic Acids Res , vol.30 , pp. 5579-5592
    • Journet, E.1    van Tuinen, D.2    Gouzy, J.3
  • 42
    • 2942589051 scopus 로고    scopus 로고
    • Predotar: A tool for rapidly screening proteomes for n-terminal targeting sequences
    • Small I, Peeters N, Legeai F, Lurin C. Predotar: a tool for rapidly screening proteomes for n-terminal targeting sequences. Pro-teomics 2004; 4: 1581-1590.
    • (2004) Pro-teomics , vol.4 , pp. 1581-1590
    • Small, I.1    Peeters, N.2    Legeai, F.3    Lurin, C.4
  • 43
    • 35748962026 scopus 로고    scopus 로고
    • The genome projects of the plant pathogenic fungi Botrytis cinerea and Sclerotinia scle-rotiorum
    • In: Jeandet P, Clément C, Conreux A, Technique & Documentation, Paris
    • Fillinger S, Amselem J, Artiguenave F, et al. The genome projects of the plant pathogenic fungi Botrytis cinerea and Sclerotinia scle-rotiorum. In: Jeandet P, Clément C, Conreux A Eds, Macromolecules and Secondary Metabolties of Grapevine and Wine. Technique & Documentation, Paris, 2007; 125-133.
    • (2007) Macromolecules and Secondary Metabolties of Grapevine and Wine , pp. 125-133
    • Fillinger, S.1    Amselem, J.2    Artiguenave, F.3
  • 44
    • 33748760611 scopus 로고    scopus 로고
    • The genome of black cot-tonwood, Populus trichocarpa (Torr. & Gray)
    • Tuskan GA, Difazio S, Jansson S, et al. The genome of black cot-tonwood, Populus trichocarpa (Torr. & Gray). Science 2006; 313: 1596-1604.
    • (2006) Science , vol.313 , pp. 1596-1604
    • Tuskan, G.A.1    Difazio, S.2    Jansson, S.3
  • 45
    • 33746830079 scopus 로고    scopus 로고
    • Genome analysis of the smallest free-living eukaryote ostreococcus tauri unveils many unique features
    • Derelle E, Ferraz C, Rombauts S, et al. Genome analysis of the smallest free-living eukaryote ostreococcus tauri unveils many unique features. Proc Natl Acad Sci USA 2006; 103: 11647-11652.
    • (2006) Proc Natl Acad Sci USA , vol.103 , pp. 11647-11652
    • Derelle, E.1    Ferraz, C.2    Rombauts, S.3
  • 46
    • 34250689932 scopus 로고    scopus 로고
    • The tiny eukaryote ostreo-coccus provides genomic insights into the paradox of plankton spe-ciation
    • Palenik B, Grimwood J, Aerts A, et al. The tiny eukaryote ostreo-coccus provides genomic insights into the paradox of plankton spe-ciation. Proc Natl Acad Sci USA 2007; 104: 7705-7710.
    • (2007) Proc Natl Acad Sci USA , vol.104 , pp. 7705-7710
    • Palenik, B.1    Grimwood, J.2    Aerts, A.3
  • 48
    • 0141905891 scopus 로고    scopus 로고
    • Improving the Arabidopsis genome annotation using maximal transcript alignment assemblies
    • Haas BJ, Delcher AL, Mount SM, et al. Improving the Arabidopsis genome annotation using maximal transcript alignment assemblies. Nucleic Acids Res 2003; 31: 5654-5666.
    • (2003) Nucleic Acids Res , vol.31 , pp. 5654-5666
    • Haas, B.J.1    Delcher, A.L.2    Mount, S.M.3


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