메뉴 건너뛰기




Volumn 7, Issue , 2006, Pages

Automatic generation of gene finders for eukaryotic species

Author keywords

[No Author keywords available]

Indexed keywords

AUTOMATIC GENERATION; DISCRETE PHASE-TYPE DISTRIBUTION; EUKARYOTIC GENOME; EUKARYOTIC SPECIES; GENE ANNOTATION; GENE STRUCTURE; LENGTH DISTRIBUTIONS; SEQUENCE LENGTH DISTRIBUTIONS;

EID: 33847166601     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-7-263     Document Type: Article
Times cited : (22)

References (41)
  • 1
    • 0031586003 scopus 로고    scopus 로고
    • Prediction of complete gene structures in human genomic DNA
    • 9149143
    • Burge C Karlin S Prediction of complete gene structures in human genomic DNA J Mol Biol 1997 268 78-94 9149143
    • (1997) J Mol Biol , vol.268 , pp. 78-94
    • Burge, C.1    Karlin, S.2
  • 2
    • 2942527473 scopus 로고    scopus 로고
    • Gene prediction with a hidden Markov model and a new intron submodel
    • Stanke M Waack S Gene prediction with a hidden Markov model and a new intron submodel Bioinformatics 2003 19 Suppl 2 11215-11225
    • (2003) Bioinformatics , vol.19 , Issue.SUPPL. 2 , pp. 11215-11225
    • Stanke, M.1    Waack, S.2
  • 3
    • 0030623944 scopus 로고    scopus 로고
    • Two methods for improving performance of an HMM and their application for gene finding
    • 9322033
    • Krogh A Two methods for improving performance of an HMM and their application for gene finding Proc Int Conf Intell Syst Mol Biol 1997 5 179-186 9322033
    • (1997) Proc Int Conf Intell Syst Mol Biol , vol.5 , pp. 179-186
    • Krogh, A.1
  • 4
    • 0034066018 scopus 로고    scopus 로고
    • Using database matches with for HMMGene for automated gene detection in Drosophila
    • 310864 10779492
    • Krogh A Using database matches with for HMMGene for automated gene detection in Drosophila Genome Res 2000 10 4 523-528 310864 10779492
    • (2000) Genome Res , vol.10 , Issue.4 , pp. 523-528
    • Krogh, A.1
  • 5
    • 29144453390 scopus 로고    scopus 로고
    • Gene identification in novel eukaryotic genomes by self-training algorithm
    • 1298918 16314312
    • Lomsadze A Ter-Hovhannisyan V Chernoff YO Borodovsky M Gene identification in novel eukaryotic genomes by self-training algorithm Nucleic Acids Res 2005 33 20 6494-6506 1298918 16314312
    • (2005) Nucleic Acids Res , vol.33 , Issue.20 , pp. 6494-6506
    • Lomsadze, A.1    Ter-Hovhannisyan, V.2    Chernoff, Y.O.3    Borodovsky, M.4
  • 6
    • 0034022596 scopus 로고    scopus 로고
    • Genie - Gene finding in Drosophila melanogaster
    • 310881 10779493
    • Reese MG Kulp D Tammana H Haussler D Genie - gene finding in Drosophila melanogaster Genome Res 2000 10 4 529-538 310881 10779493
    • (2000) Genome Res , vol.10 , Issue.4 , pp. 529-538
    • Reese, M.G.1    Kulp, D.2    Tammana, H.3    Haussler, D.4
  • 7
    • 8844252293 scopus 로고    scopus 로고
    • TigrScan and GlimmerHMM: Two open source ab initio eukaryotic gene-finders
    • 15145805
    • Majoros WH Pertea M Salzberg SL TigrScan and GlimmerHMM: Two open source ab initio eukaryotic gene-finders Bioinformatics 2004 20 16 2878-2879 15145805
    • (2004) Bioinformatics , vol.20 , Issue.16 , pp. 2878-2879
    • Majoros, W.H.1    Pertea, M.2    Salzberg, S.L.3
  • 8
    • 0041620262 scopus 로고    scopus 로고
    • GlimmerM, Exonomy and Unveil: Three ab initio eukaryotic genefinders
    • 168934 12824375
    • Majoros WH Pertea M Antonescu C Salzberg SL GlimmerM, Exonomy and Unveil: Three ab initio eukaryotic genefinders Nucleic Acids Res 2003 31 13 3601-3604 168934 12824375
    • (2003) Nucleic Acids Res , vol.31 , Issue.13 , pp. 3601-3604
    • Majoros, W.H.1    Pertea, M.2    Antonescu, C.3    Salzberg, S.L.4
  • 9
    • 2942544417 scopus 로고    scopus 로고
    • Gene finding in novel genomes
    • 421630 15144565
    • Korf I Gene finding in novel genomes BMC Bioinformatics 2004 5 59 421630 15144565
    • (2004) BMC Bioinformatics , vol.5 , pp. 59
    • Korf, I.1
  • 11
    • 0034061137 scopus 로고    scopus 로고
    • GenelD in Drosophila
    • 310871 10779490
    • Parra G Blanco E Guigo R GenelD in Drosophila Genome Res 2000 10 4 511-515 310871 10779490
    • (2000) Genome Res , vol.10 , Issue.4 , pp. 511-515
    • Parra, G.1    Blanco, E.2    Guigo, R.3
  • 13
    • 0031027525 scopus 로고    scopus 로고
    • Identification of protein coding regions in the human genome by quadratic discriminant analysis
    • 19553 9012824
    • Zhang MQ Identification of protein coding regions in the human genome by quadratic discriminant analysis Proc Natl Acad Sci USA 1997 94 2 565-568 19553 9012824
    • (1997) Proc Natl Acad Sci USA , vol.94 , Issue.2 , pp. 565-568
    • Zhang, M.Q.1
  • 14
    • 0037350957 scopus 로고    scopus 로고
    • SLAM: Cross-species gene finding and alignment with a generalized pair hidden Markov model
    • 430255 12618381
    • Alexandersson M Cawley S Pachter L SLAM: Cross-species gene finding and alignment with a generalized pair hidden Markov model Genome Res 2003 13 3 496-502 430255 12618381
    • (2003) Genome Res , vol.13 , Issue.3 , pp. 496-502
    • Alexandersson, M.1    Cawley, S.2    Pachter, L.3
  • 16
    • 17444437765 scopus 로고    scopus 로고
    • Integrating genomic homology into gene structure prediction
    • 11473003
    • Korf I Flicek P Duan D Brent MR Integrating genomic homology into gene structure prediction Bioinformatics 2001 17 Suppl 1 S140-S148 11473003
    • (2001) Bioinformatics , vol.17 , Issue.SUPPL. 1
    • Korf, I.1    Flicek, P.2    Duan, D.3    Brent, M.R.4
  • 17
    • 0036772510 scopus 로고    scopus 로고
    • Comparative ab initio prediction of gene structures using pair HMMs
    • 12376375
    • Meyer IM Durbin R Comparative ab initio prediction of gene structures using pair HMMs Bioinformatics 2002 18 10 1309-1318 12376375
    • (2002) Bioinformatics , vol.18 , Issue.10 , pp. 1309-1318
    • Meyer, I.M.1    Durbin, R.2
  • 18
    • 0037311782 scopus 로고    scopus 로고
    • Gene finding with a hidden Markov model of genome structure and evolution
    • 12538242
    • Pedersen JS Hein J Gene finding with a hidden Markov model of genome structure and evolution Bioinformatics 2003 19 2 219-227 12538242
    • (2003) Bioinformatics , vol.19 , Issue.2 , pp. 219-227
    • Pedersen, J.S.1    Hein, J.2
  • 20
    • 19844374535 scopus 로고    scopus 로고
    • Begin at the beginning: Predicting genes with 5′ UTRs
    • 1088303 15867435
    • Brown RH Gross SS Brent MR Begin at the beginning: Predicting genes with 5′ UTRs Genome Res 2005 15 5 742-747 1088303 15867435
    • (2005) Genome Res , vol.15 , Issue.5 , pp. 742-747
    • Brown, R.H.1    Gross, S.S.2    Brent, M.R.3
  • 21
    • 0642307369 scopus 로고    scopus 로고
    • EasyGene - A prokaryotic gene finder that ranks ORFs by statistical significance
    • 521197 12783628
    • Larsen T.S. Krogh A. EasyGene - A prokaryotic gene finder that ranks ORFs by statistical significance BMC Bioinformatics 2003 4 21 521197 12783628
    • (2003) BMC Bioinformatics , vol.4 , pp. 21
    • Larsen, T.S.1    Krogh, A.2
  • 22
    • 0032518163 scopus 로고    scopus 로고
    • Microbial gene identification using interpolated Markov models
    • 147303 9421513
    • Salzberg SL Delcher AL Kasif S White O Microbial gene identification using interpolated Markov models Nucleic Acids Res 1998 26 2 544-548 147303 9421513
    • (1998) Nucleic Acids Res , vol.26 , Issue.2 , pp. 544-548
    • Salzberg, S.L.1    Delcher, A.L.2    Kasif, S.3    White, O.4
  • 24
    • 0033214628 scopus 로고    scopus 로고
    • Heuristic approach to deriving models for gene finding
    • 148655 10481031
    • Besemer J Borodovsky M Heuristic approach to deriving models for gene finding Nucleic Acids Res 1999 27 19 3911-3920 148655 10481031
    • (1999) Nucleic Acids Res , vol.27 , Issue.19 , pp. 3911-3920
    • Besemer, J.1    Borodovsky, M.2
  • 25
    • 0035875343 scopus 로고    scopus 로고
    • GeneMarkS: A self-training method for prediction of gene starts in microbial genomes. Implications for finding sequence motifs in regulatory regions
    • 55746 11410670
    • Besemer J Lomsadze A Borodovsky M GeneMarkS: A self-training method for prediction of gene starts in microbial genomes. Implications for finding sequence motifs in regulatory regions Nucleic Acids Res 2001 29 12 2607-2618 55746 11410670
    • (2001) Nucleic Acids Res , vol.29 , Issue.12 , pp. 2607-2618
    • Besemer, J.1    Lomsadze, A.2    Borodovsky, M.3
  • 26
    • 0032519353 scopus 로고    scopus 로고
    • GeneMark.hmm: New solutions for gene finding
    • 147337 9461475
    • Lukashin AV Borodovsky M GeneMark.hmm: New solutions for gene finding Nucleic Acids Res 1998 26 4 1107-1115 147337 9461475
    • (1998) Nucleic Acids Res , vol.26 , Issue.4 , pp. 1107-1115
    • Lukashin, A.V.1    Borodovsky, M.2
  • 28
    • 2342623940 scopus 로고    scopus 로고
    • Analysis and recognition of 5′ UTR intron splice sites in human pre-mRNA
    • 373407 14960723
    • Eden E Brunak S Analysis and recognition of 5′ UTR intron splice sites in human pre-mRNA Nucleic Acids Res 2004 32 3 1131-1142 373407 14960723
    • (2004) Nucleic Acids Res , vol.32 , Issue.3 , pp. 1131-1142
    • Eden, E.1    Brunak, S.2
  • 29
    • 0024610919 scopus 로고
    • A tutorial on hidden Markov models and selected applications in speech recognition
    • Rabiner LR A tutorial on hidden Markov models and selected applications in speech recognition Proc IEEE 1989 77 2 257-286
    • (1989) Proc IEEE , vol.77 , Issue.2 , pp. 257-286
    • Rabiner, L.R.1
  • 30
    • 0043123281 scopus 로고    scopus 로고
    • Acyclic discrete phase type distributions: Properties and a parameter estimation algorithm
    • Bobbio A Horvath A Scarpa Telek M Acyclic discrete phase type distributions: Properties and a parameter estimation algorithm Performance Evaluation 2003 54 1-32
    • (2003) Performance Evaluation , vol.54 , pp. 1-32
    • Bobbio, A.1    Horvath, A.2    Scarpa3    Telek, M.4
  • 32
    • 0033967692 scopus 로고    scopus 로고
    • Introducing RefSeq and LocusLink: Curated human genome resources at the NCBI
    • 10637631
    • Pruitt KD Katz KS Sicotte H Maglott DR Introducing RefSeq and LocusLink: curated human genome resources at the NCBI Trends Genet 2000 16 44-47 10637631
    • (2000) Trends Genet , vol.16 , pp. 44-47
    • Pruitt, K.D.1    Katz, K.S.2    Sicotte, H.3    Maglott, D.R.4
  • 33
    • 0036226603 scopus 로고    scopus 로고
    • BLAT-the BLAST-like alignment tool
    • 187518 11932250
    • Kent WJ BLAT-the BLAST-like alignment tool Genome Res 2002 12 4 656-664 187518 11932250
    • (2002) Genome Res , vol.12 , Issue.4 , pp. 656-664
    • Kent, W.J.1
  • 34
    • 0030870076 scopus 로고    scopus 로고
    • EST_GENOME: A program to align spliced DNA sequences to unspliced genomic DNA
    • 9283765
    • Mott R EST_GENOME: A program to align spliced DNA sequences to unspliced genomic DNA Comput Appl Biosci 1997 13 4 477-478 9283765
    • (1997) Comput Appl Biosci , vol.13 , Issue.4 , pp. 477-478
    • Mott, R.1
  • 35
    • 0036682115 scopus 로고    scopus 로고
    • Analysis of the role of Caenorhabditis elegans GC-AG introns in regulated splicing
    • 137088 12140320
    • Farrer T Roller AB Kent WJ Zahler AM Analysis of the role of Caenorhabditis elegans GC-AG introns in regulated splicing Nucleic Acids Res 2002 30 15 3360-3367 137088 12140320
    • (2002) Nucleic Acids Res , vol.30 , Issue.15 , pp. 3360-3367
    • Farrer, T.1    Roller, A.B.2    Kent, W.J.3    Zahler, A.M.4
  • 36
    • 0035875551 scopus 로고    scopus 로고
    • Human GC-AG alternative intron isoforms with weak donor sites show enhanced consensus at acceptor exon positions
    • 55748 11410667
    • Thanaraj TA Clark F Human GC-AG alternative intron isoforms with weak donor sites show enhanced consensus at acceptor exon positions Nucleic Acids Res 2001 29 12 2581-2593 55748 11410667
    • (2001) Nucleic Acids Res , vol.29 , Issue.12 , pp. 2581-2593
    • Thanaraj, T.A.1    Clark, F.2
  • 37
    • 0027092678 scopus 로고
    • Selection of representative protein data sets
    • 1304348
    • Hobohm U Scharf M Schneider R Sander C Selection of representative protein data sets Protein Sci 1992 1 3 409-417 1304348
    • (1992) Protein Sci , vol.1 , Issue.3 , pp. 409-417
    • Hobohm, U.1    Scharf, M.2    Schneider, R.3    Sander, C.4
  • 38
    • 84886762732 scopus 로고    scopus 로고
    • Gish W 1996 http://blast.wustl.edu
    • (1996)
    • Gish, W.1
  • 39
    • 0025008168 scopus 로고
    • Sequence logos: A new way to display consensus sequences
    • 332411 2172928
    • Schneider TD Stephens RM Sequence logos: A new way to display consensus sequences Nucleic Acids Res 1990 18 20 6097-6100 332411 2172928
    • (1990) Nucleic Acids Res , vol.18 , Issue.20 , pp. 6097-6100
    • Schneider, T.D.1    Stephens, R.M.2
  • 40
    • 84886764896 scopus 로고    scopus 로고
    • Agene web site http://www.binf.ku.dk/services/agene
  • 41
    • 0035735265 scopus 로고    scopus 로고
    • Computational identification of promoters and first exons in the human genome
    • 11726928
    • Davuluri RV Grosse I Zhang MQ Computational identification of promoters and first exons in the human genome Nat Genet 2001 29 4 412-417 11726928
    • (2001) Nat Genet , vol.29 , Issue.4 , pp. 412-417
    • Davuluri, R.V.1    Grosse, I.2    Zhang, M.Q.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.