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Volumn 13, Issue 5, 2012, Pages 329-342

A beginner's guide to eukaryotic genome annotation

Author keywords

[No Author keywords available]

Indexed keywords

AB INITIO CALCULATION; ACCURACY; EUKARYOTIC GENOME ANNOTATION; GENETIC DATABASE; HUMAN; MOLECULAR GENETICS; NONHUMAN; NUCLEOTIDE SEQUENCE; PREDICTION; PRIORITY JOURNAL; PROTEIN ASSEMBLY; QUALITY CONTROL; REVIEW; SENSITIVITY AND SPECIFICITY; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS;

EID: 84859898660     PISSN: 14710056     EISSN: 14710064     Source Type: Journal    
DOI: 10.1038/nrg3174     Document Type: Review
Times cited : (446)

References (143)
  • 1
    • 0034708480 scopus 로고    scopus 로고
    • The genome sequence of Drosophila melanogaster
    • Adams, M. D. et al. The genome sequence of Drosophila melanogaster. Science 287, 2185-2195 (2000).
    • (2000) Science , vol.287 , pp. 2185-2195
    • Adams, M.D.1
  • 2
    • 0012340085 scopus 로고    scopus 로고
    • Finishing a whole-genome shotgun: Release 3 of the Drosophila melanogaster euchromatic genome sequence
    • research0079
    • Celniker, S. E. et al. Finishing a whole-genome shotgun: release 3 of the Drosophila melanogaster euchromatic genome sequence. Genome Biol. 3, research0079 (2002).
    • (2002) Genome Biol. , vol.3
    • Celniker, S.E.1
  • 3
    • 0035895505 scopus 로고    scopus 로고
    • The sequence of the human genome
    • Venter, J. C. et al. The sequence of the human genome. Science 291, 1304-1351 (2001).
    • (2001) Science , vol.291 , pp. 1304-1351
    • Venter, J.C.1
  • 4
    • 7244245762 scopus 로고    scopus 로고
    • Finishing the euchromatic sequence of the human genome
    • Finishing the euchromatic sequence of the human genome. Nature 431, 931-945 (2004).
    • (2004) Nature , vol.431 , pp. 931-945
  • 5
    • 58149513263 scopus 로고    scopus 로고
    • Annotating genomes with massive-scale RNA sequencing
    • Denoeud, F. et al. Annotating genomes with massive-scale RNA sequencing. Genome Biol. 9, R175 (2008).
    • (2008) Genome Biol. , vol.9
    • Denoeud, F.1
  • 6
    • 70349956497 scopus 로고    scopus 로고
    • Direct RNA sequencing
    • Ozsolak, F. et al. Direct RNA sequencing. Nature 461, 814-818 (2009).
    • (2009) Nature , vol.461 , pp. 814-818
    • Ozsolak, F.1
  • 8
    • 56549101959 scopus 로고    scopus 로고
    • Alternative isoform regulation in human tissue transcriptomes
    • This paper provides one of the most extensively documented surveys of alternatively spliced transcripts. It is a key publication for understanding how extensive alternative splicing is in human tissues, for understanding how powerful RNA-seq data are as a tool for discovering new transcripts and for quantifying their abundance and differential expression patterns
    • Wang, E. T. et al. Alternative isoform regulation in human tissue transcriptomes. Nature 456, 470-476 (2008). This paper provides one of the most extensively documented surveys of alternatively spliced transcripts. It is a key publication for understanding how extensive alternative splicing is in human tissues, for understanding how powerful RNA-seq data are as a tool for discovering new transcripts and for quantifying their abundance and differential expression patterns.
    • (2008) Nature , vol.456 , pp. 470-476
    • Wang, E.T.1
  • 9
    • 70349866672 scopus 로고    scopus 로고
    • Genomics. Genome project standards in a new era of sequencing
    • Chain, P. S. et al. Genomics. Genome project standards in a new era of sequencing. Science 326, 236-237 (2009).
    • (2009) Science , vol.326 , pp. 236-237
    • Chain, P.S.1
  • 10
    • 38049057159 scopus 로고    scopus 로고
    • MAKER: An easy-to-use annotation pipeline designed for emerging model organism genomes
    • Cantarel, B. L. et al. MAKER: an easy-to-use annotation pipeline designed for emerging model organism genomes. Genome Res. 18, 188-196 (2008).
    • (2008) Genome Res. , vol.18 , pp. 188-196
    • Cantarel, B.L.1
  • 11
    • 79953192561 scopus 로고    scopus 로고
    • A vertebrate case study of the quality of assemblies derived from next-generation sequences
    • Ye, L. et al. A vertebrate case study of the quality of assemblies derived from next-generation sequences. Genome Biol. 12, R31 (2011).
    • (2011) Genome Biol. , vol.12
    • Ye, L.1
  • 12
    • 34249848751 scopus 로고    scopus 로고
    • CEGMA: A pipeline to accurately annotate core genes in eukaryotic genomes
    • Parra, G., Bradnam, K. & Korf, I. CEGMA: a pipeline to accurately annotate core genes in eukaryotic genomes. Bioinformatics 23, 1061-1067 (2007).
    • (2007) Bioinformatics , vol.23 , pp. 1061-1067
    • Parra, G.1    Bradnam, K.2    Korf, I.3
  • 13
    • 77950658346 scopus 로고    scopus 로고
    • Improving draft assemblies by iterative mapping and assembly of short reads to eliminate gaps
    • Tsai, I. J., Otto, T. D. & Berriman, M. Improving draft assemblies by iterative mapping and assembly of short reads to eliminate gaps. Genome Biol. 11, R41 (2010).
    • (2010) Genome Biol. , vol.11
    • Tsai, I.J.1    Otto, T.D.2    Berriman, M.3
  • 14
    • 67650735586 scopus 로고    scopus 로고
    • ABACAS: Algorithm-based automatic contiguation of assembled sequences
    • Assefa, S., Keane, T. M., Otto, T. D., Newbold, C. &Berriman, M. ABACAS: algorithm-based automatic contiguation of assembled sequences. Bioinformatics 25, 1968-1969 (2009).
    • (2009) Bioinformatics , vol.25 , pp. 1968-1969
    • Assefa, S.1    Keane, T.M.2    Otto, T.D.3    Newbold, C.4    Berriman, M.5
  • 15
    • 77949515650 scopus 로고    scopus 로고
    • R2cat: Synteny plots and comparative assembly
    • Husemann, P. & Stoye, J. r2cat: synteny plots and comparative assembly. Bioinformatics 26, 570-571 (2010).
    • (2010) Bioinformatics , vol.26 , pp. 570-571
    • Husemann, P.1    Stoye, J.2
  • 16
    • 0038709269 scopus 로고    scopus 로고
    • A novel class of SINE elements derived from 5S rRNA
    • Kapitonov, V. V. & Jurka, J. A novel class of SINE elements derived from 5S rRNA. Mol. Biol. Evol. 20, 694-702 (2003).
    • (2003) Mol. Biol. Evol. , vol.20 , pp. 694-702
    • Kapitonov, V.V.1    Jurka, J.2
  • 17
    • 42349111552 scopus 로고    scopus 로고
    • A universal classification of eukaryotic transposable elements implemented in Repbase
    • author reply 414
    • Kapitonov, V. V. & Jurka, J. A universal classification of eukaryotic transposable elements implemented in Repbase. Nature Rev. Genet. 9, 411-412; author reply 414 (2008).
    • (2008) Nature Rev. Genet. , vol.9 , pp. 411-412
    • Kapitonov, V.V.1    Jurka, J.2
  • 18
    • 2042437650 scopus 로고    scopus 로고
    • Initial sequencing and analysis of the human genome
    • Lander, E. S. et al. Initial sequencing and analysis of the human genome. Nature 409, 860-921 (2001).
    • (2001) Nature , vol.409 , pp. 860-921
    • Lander, E.S.1
  • 19
    • 42149187766 scopus 로고    scopus 로고
    • Improved detection and annotation of transposable elements in sequenced genomes using multiple reference sequence sets
    • Buisine, N., Quesneville, H. & Colot, V. Improved detection and annotation of transposable elements in sequenced genomes using multiple reference sequence sets. Genomics 91, 467-475 (2008).
    • (2008) Genomics , vol.91 , pp. 467-475
    • Buisine, N.1    Quesneville, H.2    Colot, V.3
  • 20
    • 78650432054 scopus 로고    scopus 로고
    • MITE-Hunter: A program for discovering miniature inverted-repeat transposable elements from genomic sequences
    • Han, Y. & Wessler, S. R. MITE-Hunter: a program for discovering miniature inverted-repeat transposable elements from genomic sequences. Nucleic Acids Res. 38, e199 (2010).
    • (2010) Nucleic Acids Res. , vol.38
    • Han, Y.1    Wessler, S.R.2
  • 21
    • 15244354523 scopus 로고    scopus 로고
    • Automated characterization of potentially active retroid agents in the human genome
    • McClure, M. A. et al. Automated characterization of potentially active retroid agents in the human genome. Genomics 85, 512-523 (2005).
    • (2005) Genomics , vol.85 , pp. 512-523
    • McClure, M.A.1
  • 22
    • 0036673472 scopus 로고    scopus 로고
    • Automated de novo identification of repeat sequence families in sequenced genomes
    • Bao, Z. & Eddy, S. R. Automated de novo identification of repeat sequence families in sequenced genomes. Genome Res. 12, 1269-1276 (2002).
    • (2002) Genome Res. , vol.12 , pp. 1269-1276
    • Bao, Z.1    Eddy, S.R.2
  • 23
    • 29144455282 scopus 로고    scopus 로고
    • De novo identification of repeat families in large genomes
    • Price, A. L., Jones, N. C. & Pevzner, P. A. De novo identification of repeat families in large genomes. Bioinformatics 21 (Suppl. 1), i351-i358 (2005).
    • (2005) Bioinformatics , vol.21 , Issue.SUPPL. 1
    • Price, A.L.1    Jones, N.C.2    Pevzner, P.A.3
  • 25
  • 26
    • 83855165105 scopus 로고    scopus 로고
    • Repetitive DNA and next-generation sequencing: Computational challenges and solutions
    • Treangen, T. J. & Salzberg, S. L. Repetitive DNA and next-generation sequencing: computational challenges and solutions. Nature Rev. Genet. 13, 36-46 (2012).
    • (2012) Nature Rev. Genet. , vol.13 , pp. 36-46
    • Treangen, T.J.1    Salzberg, S.L.2
  • 27
    • 36549035839 scopus 로고    scopus 로고
    • Discovering and detecting transposable elements in genome sequences
    • Bergman, C. M. & Quesneville, H. Discovering and detecting transposable elements in genome sequences. Brief. Bioinform. 8, 382-392 (2007).
    • (2007) Brief. Bioinform. , vol.8 , pp. 382-392
    • Bergman, C.M.1    Quesneville, H.2
  • 28
    • 70349318211 scopus 로고    scopus 로고
    • The impact of retrotransposons on human genome evolution
    • Cordaux, R. & Batzer, M. A. The impact of retrotransposons on human genome evolution. Nature Rev. Genet. 10, 691-703 (2009).
    • (2009) Nature Rev. Genet. , vol.10 , pp. 691-703
    • Cordaux, R.1    Batzer, M.A.2
  • 29
    • 71549123707 scopus 로고    scopus 로고
    • Alu repeats increase local recombination rates
    • Witherspoon, D. J. et al. Alu repeats increase local recombination rates. BMC Genomics 10, 530 (2009).
    • (2009) BMC Genomics , vol.10 , pp. 530
    • Witherspoon, D.J.1
  • 32
    • 2442649543 scopus 로고    scopus 로고
    • O'Reilly & Associates, Everyone involved with a genome project should be familiar with BLAST. Reference 31 is the original paper describing this tool. Reference 32 is an entire book describing BLAST and how it is used
    • Korf, I., Yandell, M. & Bedell, J. BLAST: an Essential Guide to the Basic Local Alignment Search Tool 339 (O'Reilly & Associates, 2003). Everyone involved with a genome project should be familiar with BLAST. Reference 31 is the original paper describing this tool. Reference 32 is an entire book describing BLAST and how it is used.
    • (2003) BLAST: An Essential Guide to the Basic Local Alignment Search Tool , vol.339
    • Korf, I.1    Yandell, M.2    Bedell, J.3
  • 33
    • 0030801002 scopus 로고    scopus 로고
    • Gapped BLAST and PSI-BLAST: A new generation of protein database search programs
    • Altschul, S. F. et al. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25, 3389-3402 (1997).
    • (1997) Nucleic Acids Res. , vol.25 , pp. 3389-3402
    • Altschul, S.F.1
  • 34
    • 84859908031 scopus 로고
    • Crossmatch. A general purpose utility for comparing any two sets of DNA sequences
    • Green, P. Crossmatch. A general purpose utility for comparing any two sets of DNA sequences. PHRAP [online], http://www.phrap.org/phredphrap/general. html (1993-1996).
    • (1993) PHRAP [Online]
    • Green, P.1
  • 36
    • 74049108922 scopus 로고    scopus 로고
    • BLAST+: Architecture and applications
    • Camacho, C. et al. BLAST+: architecture and applications. BMC Bioinformatics 10, 421 (2009).
    • (2009) BMC Bioinformatics , vol.10 , pp. 421
    • Camacho, C.1
  • 38
    • 28044431588 scopus 로고    scopus 로고
    • Protein variety and functional diversity: Swiss-Prot annotation in its biological context
    • Boeckmann, B. et al. Protein variety and functional diversity: Swiss-Prot annotation in its biological context. C.R. Biol. 328, 882-899 (2005).
    • (2005) C.R. Biol. , vol.328 , pp. 882-899
    • Boeckmann, B.1
  • 39
    • 78651319979 scopus 로고    scopus 로고
    • Ongoing and future developments at the Universal Protein Resource
    • The UniProt Consortium
    • The UniProt Consortium. Ongoing and future developments at the Universal Protein Resource. Nucleic Acids Res. 39, D214-D219 (2011).
    • (2011) Nucleic Acids Res. , vol.39
  • 41
    • 58149200954 scopus 로고    scopus 로고
    • Database resources of the National Center for Biotechnology Information
    • Sayers, E. W. et al. Database resources of the National Center for Biotechnology Information. Nucleic Acids Res. 37, D5-D15 (2009).
    • (2009) Nucleic Acids Res. , vol.37
    • Sayers, E.W.1
  • 42
    • 0036226603 scopus 로고    scopus 로고
    • BLAT-the BLAST-like alignment tool
    • Kent, W. J. BLAT-the BLAST-like alignment tool. Genome Res. 12, 656-664 (2002).
    • (2002) Genome Res. , vol.12 , pp. 656-664
    • Kent, W.J.1
  • 43
    • 24044447664 scopus 로고    scopus 로고
    • Automated generation of heuristics for biological sequence comparison
    • Slater, G. S. & Birney, E. Automated generation of heuristics for biological sequence comparison. BMC Bioinformatics 6, 31 (2005).
    • (2005) BMC Bioinformatics , vol.6 , pp. 31
    • Slater, G.S.1    Birney, E.2
  • 44
    • 46649115430 scopus 로고    scopus 로고
    • Splign: Algorithms for computing spliced alignments with identification of paralogs
    • Kapustin, Y., Souvorov, A., Tatusova, T. & Lipman, D. Splign: algorithms for computing spliced alignments with identification of paralogs. Biol. Direct 3, 20 (2008).
    • (2008) Biol. Direct , vol.3 , pp. 20
    • Kapustin, Y.1    Souvorov, A.2    Tatusova, T.3    Lipman, D.4
  • 45
    • 0035189310 scopus 로고    scopus 로고
    • Spidey: A tool for mRNA-to-genomic alignments
    • Wheelan, S. J., Church, D. M. & Ostell, J. M. Spidey: a tool for mRNA-to-genomic alignments. Genome Res. 11, 1952-1957 (2001).
    • (2001) Genome Res. , vol.11 , pp. 1952-1957
    • Wheelan, S.J.1    Church, D.M.2    Ostell, J.M.3
  • 46
    • 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, G. M. &Miller, W. A computer program for aligning a cDNA sequence with a genomic DNA sequence. Genome Res. 8, 967-974 (1998).
    • (1998) Genome Res. , vol.8 , pp. 967-974
    • Florea, L.1    Hartzell, G.2    Zhang, Z.3    Rubin, G.M.4    Miller, W.5
  • 47
    • 79957842166 scopus 로고    scopus 로고
    • Computational methods for transcriptome annotation and quantification using RNA-seq
    • Garber, M., Grabherr, M. G., Guttman, M. &Trapnell, C. Computational methods for transcriptome annotation and quantification using RNA-seq. Nature Methods 8, 469-477 (2011).
    • (2011) Nature Methods , vol.8 , pp. 469-477
    • Garber, M.1    Grabherr, M.G.2    Guttman, M.3    Trapnell, C.4
  • 48
    • 66449136667 scopus 로고    scopus 로고
    • ABySS: A parallel assembler for short read sequence data
    • Simpson, J. T. et al. ABySS: a parallel assembler for short read sequence data. Genome Res. 19, 1117-1123 (2009).
    • (2009) Genome Res. , vol.19 , pp. 1117-1123
    • Simpson, J.T.1
  • 49
    • 75649124547 scopus 로고    scopus 로고
    • De novo assembly of human genomes with massively parallel short read sequencing
    • Li, R. et al. De novo assembly of human genomes with massively parallel short read sequencing. Genome Res. 20, 265-272 (2010).
    • (2010) Genome Res. , vol.20 , pp. 265-272
    • Li, R.1
  • 50
    • 79960264362 scopus 로고    scopus 로고
    • Full-length transcriptome assembly from RNA-seq data without a reference genome
    • This paper describes Trinity, a transcriptome assembler that was specifically designed for next-generation sequence data. It is required reading for anyone trying to use RNA-seq data for genome annotation
    • Grabherr, M. G. et al. Full-length transcriptome assembly from RNA-seq data without a reference genome. Nature Biotech. 29, 644-652 (2011). This paper describes Trinity, a transcriptome assembler that was specifically designed for next-generation sequence data. It is required reading for anyone trying to use RNA-seq data for genome annotation.
    • (2011) Nature Biotech. , vol.29 , pp. 644-652
    • Grabherr, M.G.1
  • 51
    • 65449136284 scopus 로고    scopus 로고
    • TopHat: Discovering splice junctions with RNA-seq
    • Trapnell, C., Pachter, L. & Salzberg, S. L. TopHat: discovering splice junctions with RNA-seq. Bioinformatics 25, 1105-1111 (2009).
    • (2009) Bioinformatics , vol.25 , pp. 1105-1111
    • Trapnell, C.1    Pachter, L.2    Salzberg, S.L.3
  • 52
    • 77951820899 scopus 로고    scopus 로고
    • Fast and SNP-tolerant detection of complex variants and splicing in short reads
    • Wu, T. D. & Nacu, S. Fast and SNP-tolerant detection of complex variants and splicing in short reads. Bioinformatics 26, 873-881 (2010).
    • (2010) Bioinformatics , vol.26 , pp. 873-881
    • Wu, T.D.1    Nacu, S.2
  • 53
    • 77952148742 scopus 로고    scopus 로고
    • Ab initio reconstruction of cell type-specific transcriptomes in mouse reveals the conserved multi-exonic structure of lincRNAs
    • Guttman, M. et al. Ab initio reconstruction of cell type-specific transcriptomes in mouse reveals the conserved multi-exonic structure of lincRNAs. Nature Biotech. 28, 503-510 (2010).
    • (2010) Nature Biotech. , vol.28 , pp. 503-510
    • Guttman, M.1
  • 54
    • 77952123055 scopus 로고    scopus 로고
    • Transcript assembly and quantification by RNA-seq reveals unannotated transcripts and isoform switching during cell differentiation
    • Trapnell, C. et al. Transcript assembly and quantification by RNA-seq reveals unannotated transcripts and isoform switching during cell differentiation. Nature Biotech. 28, 511-515 (2010).
    • (2010) Nature Biotech. , vol.28 , pp. 511-515
    • Trapnell, C.1
  • 55
    • 84859885816 scopus 로고    scopus 로고
    • Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks
    • This paper describes best practice approaches for combining TopHat and Cufflinks when using RNA-seq data for genome annotation
    • Trapnell, C. et al. Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks. Nature Protoc. 7, 562-578 (2012). This paper describes best practice approaches for combining TopHat and Cufflinks when using RNA-seq data for genome annotation.
    • (2012) Nature Protoc. , vol.7 , pp. 562-578
    • Trapnell, C.1
  • 56
    • 0141905891 scopus 로고    scopus 로고
    • Improving the Arabidopsis genome annotation using maximal transcript alignment assemblies
    • Haas, B. J. et al. Improving the Arabidopsis genome annotation using maximal transcript alignment assemblies. Nucleic Acids Res. 31, 5654-5666 (2003).
    • (2003) Nucleic Acids Res. , vol.31 , pp. 5654-5666
    • Haas, B.J.1
  • 58
    • 0028700540 scopus 로고
    • The prediction of human exons by oligonucleotide composition and discriminant analysis of spliceable open reading frames
    • Solovyev, V. V., Salamov, A. A. & Lawrence, C. B. The prediction of human exons by oligonucleotide composition and discriminant analysis of spliceable open reading frames. Proc. Int. Conf. Intell. Syst. Mol. Biol. 2, 354-362 (1994).
    • (1994) Proc. Int. Conf. Intell. Syst. Mol. Biol. , vol.2 , pp. 354-362
    • Solovyev, V.V.1    Salamov, A.A.2    Lawrence, C.B.3
  • 59
    • 0031586003 scopus 로고    scopus 로고
    • Prediction of complete gene structures in human genomic DNA
    • This study describes the ab initio gene predictor GenScan. It is a classic paper that is full of informative explanations of the problems associated with eukaryotic gene prediction
    • Burge, C. & Karlin, S. Prediction of complete gene structures in human genomic DNA. J. Mol. Biol. 268, 78-94 (1997). This study describes the ab initio gene predictor GenScan. It is a classic paper that is full of informative explanations of the problems associated with eukaryotic gene prediction.
    • (1997) J. Mol. Biol. , vol.268 , pp. 78-94
    • Burge, C.1    Karlin, S.2
  • 60
    • 0034022596 scopus 로고    scopus 로고
    • Genie-gene finding in Drosophila melanogaster
    • Reese, M. G., Kulp, D., Tammana, H. & Haussler, D. Genie-gene finding in Drosophila melanogaster. Genome Res. 10, 529-538 (2000).
    • (2000) Genome Res. , vol.10 , pp. 529-538
    • Reese, M.G.1    Kulp, D.2    Tammana, H.3    Haussler, D.4
  • 61
    • 28844443172 scopus 로고    scopus 로고
    • Genome annotation past, present, and future: How to define an ORF at each locus
    • Brent, M. R. Genome annotation past, present, and future: how to define an ORF at each locus. Genome Res. 15, 1777-1786 (2005).
    • (2005) Genome Res. , vol.15 , pp. 1777-1786
    • Brent, M.R.1
  • 62
    • 2942544417 scopus 로고    scopus 로고
    • Gene finding in novel genomes
    • This paper describes a gene predictor, SNAP, that is easy to use and to configure. It also clearly explains the pitfalls that are associated with using a poorly trained gene finder or one that has been trained on a different genome from the one that is being annotated
    • Korf, I. Gene finding in novel genomes. BMC Bioinformatics 5, 59 (2004). This paper describes a gene predictor, SNAP, that is easy to use and to configure. It also clearly explains the pitfalls that are associated with using a poorly trained gene finder or one that has been trained on a different genome from the one that is being annotated.
    • (2004) BMC Bioinformatics , vol.5 , pp. 59
    • Korf, I.1
  • 63
    • 33748671541 scopus 로고    scopus 로고
    • EGASP: Introduction
    • This is the introduction to an entire issue of Genome Biology that is dedicated to benchmarking an entire host of eukaryotic gene finders and annotation pipelines. Anyone involved with a genome annotation project should have a look at every paper in this special supplement
    • Reese, M. G. & Guigo, R. EGASP: Introduction. Genome Biol. 7 (Suppl. 1), 1-3 (2006). This is the introduction to an entire issue of Genome Biology that is dedicated to benchmarking an entire host of eukaryotic gene finders and annotation pipelines. Anyone involved with a genome annotation project should have a look at every paper in this special supplement.
    • (2006) Genome Biol. , vol.7 , Issue.SUPPL. 1 , pp. 1-3
    • Reese, M.G.1    Guigo, R.2
  • 64
    • 62149125547 scopus 로고    scopus 로고
    • NGASP-the nematode genome annotation assessment project
    • Coghlan, A. et al. nGASP-the nematode genome annotation assessment project. BMC Bioinformatics 9, 549 (2008).
    • (2008) BMC Bioinformatics , vol.9 , pp. 549
    • Coghlan, A.1
  • 65
    • 23144437736 scopus 로고    scopus 로고
    • EGASP: Collaboration through competition to find human genes
    • Guigo, R. & Reese, M. G. EGASP: collaboration through competition to find human genes. Nature Methods 2, 575-577 (2005).
    • (2005) Nature Methods , vol.2 , pp. 575-577
    • Guigo, R.1    Reese, M.G.2
  • 66
    • 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 19 (Suppl. 2), ii215-ii225 (2003).
    • (2003) Bioinformatics , vol.19 , Issue.SUPPL. 2
    • Stanke, M.1    Waack, S.2
  • 67
    • 33645161645 scopus 로고    scopus 로고
    • Gene prediction in eukaryotes with a generalized hidden Markov model that uses hints from external sources
    • Stanke, M., Schoffmann, O., Morgenstern, B. &Waack, S. Gene prediction in eukaryotes with a generalized hidden Markov model that uses hints from external sources. BMC Bioinformatics 7, 62 (2006).
    • (2006) BMC Bioinformatics , vol.7 , pp. 62
    • Stanke, M.1    Schoffmann, O.2    Morgenstern, B.3    Waack, S.4
  • 68
    • 0032519353 scopus 로고    scopus 로고
    • GeneMark.hmm: New solutions for gene finding
    • Lukashin, A. V. & Borodovsky, M. GeneMark.hmm: new solutions for gene finding. Nucleic Acids Res. 26, 1107-1115 (1998).
    • (1998) Nucleic Acids Res. , vol.26 , pp. 1107-1115
    • Lukashin, A.V.1    Borodovsky, M.2
  • 69
    • 57149099395 scopus 로고    scopus 로고
    • Gene prediction in novel fungal genomes using an ab initio algorithm with unsupervised training
    • Ter-Hovhannisyan, V., Lomsadze, A., Chernoff, Y. O. &Borodovsky, M. Gene prediction in novel fungal genomes using an ab initio algorithm with unsupervised training. Genome Res. 18, 1979-1990 (2008).
    • (2008) Genome Res. , vol.18 , pp. 1979-1990
    • Ter-Hovhannisyan, V.1    Lomsadze, A.2    Chernoff, Y.O.3    Borodovsky, M.4
  • 70
    • 77955902981 scopus 로고    scopus 로고
    • Ab initio gene identification in metagenomic sequences
    • Zhu, W., Lomsadze, A. & Borodovsky, M. Ab initio gene identification in metagenomic sequences. Nucleic Acids Res. 38, e132 (2010).
    • (2010) Nucleic Acids Res. , vol.38
    • Zhu, W.1    Lomsadze, A.2    Borodovsky, M.3
  • 71
    • 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, S140-S148 (2001).
    • (2001) Bioinformatics , vol.17
    • Korf, I.1    Flicek, P.2    Duan, D.3    Brent, M.R.4
  • 72
    • 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, 516-522 (2000).
    • (2000) Genome Res. , vol.10 , pp. 516-522
    • Salamov, A.A.1    Solovyev, V.V.2
  • 73
    • 84859881856 scopus 로고    scopus 로고
    • National Center for Biotechnology Information [online]
    • Souvorov, A. et al. Gnomon - the NCBI eukaryotic gene prediction tool. National Center for Biotechnology Information [online], http://www.ncbi.nlm.nih. gov/genome/guide/gnomon.shtml (2010).
    • (2010) Gnomon - The NCBI Eukaryotic Gene Prediction Tool
    • Souvorov, A.1
  • 74
    • 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, 1418-1427 (2002).
    • (2002) Genome Res. , vol.12 , pp. 1418-1427
    • Howe, K.L.1    Chothia, T.2    Durbin, R.3
  • 75
    • 0012302769 scopus 로고    scopus 로고
    • An integrated computational pipeline and database to support whole-genome sequence annotation
    • research0081
    • Mungall, C. J. et al. An integrated computational pipeline and database to support whole-genome sequence annotation. Genome Biol. 3, research0081 (2002).
    • (2002) Genome Biol. , vol.3
    • Mungall, C.J.1
  • 76
    • 0002636459 scopus 로고    scopus 로고
    • Annotation of the Drosophila melanogaster euchromatic genome: A systematic review
    • research0083
    • Misra, S. et al. Annotation of the Drosophila melanogaster euchromatic genome: a systematic review. Genome Biol. 3, research0083 (2002).
    • (2002) Genome Biol. , vol.3
    • Misra, S.1
  • 77
    • 13444267288 scopus 로고    scopus 로고
    • A computational and experimental approach to validating annotations and gene predictions in the Drosophila melanogaster genome
    • Yandell, M. et al. A computational and experimental approach to validating annotations and gene predictions in the Drosophila melanogaster genome. Proc. Natl Acad. Sci. USA 102, 1566-1571 (2005).
    • (2005) Proc. Natl Acad. Sci. USA , vol.102 , pp. 1566-1571
    • Yandell, M.1
  • 78
    • 24644485994 scopus 로고    scopus 로고
    • JIGSAW: Integration of multiple sources of evidence for gene prediction
    • Allen, J. E. & Salzberg, S. L. JIGSAW: integration of multiple sources of evidence for gene prediction. Bioinformatics 21, 3596-3603 (2005).
    • (2005) Bioinformatics , vol.21 , pp. 3596-3603
    • Allen, J.E.1    Salzberg, S.L.2
  • 79
    • 42949086676 scopus 로고    scopus 로고
    • Automated eukaryotic gene structure annotation using EVidenceModeler and the Program to Assemble Spliced Alignments
    • Haas, B. J. et al. Automated eukaryotic gene structure annotation using EVidenceModeler and the Program to Assemble Spliced Alignments. Genome Biol. 9, R7 (2008).
    • (2008) Genome Biol. , vol.9
    • Haas, B.J.1
  • 80
    • 34147180390 scopus 로고    scopus 로고
    • Creating a honey bee consensus gene set
    • Elsik, C. G. et al. Creating a honey bee consensus gene set. Genome Biol. 8, R13 (2007).
    • (2007) Genome Biol. , vol.8
    • Elsik, C.G.1
  • 81
    • 40049107811 scopus 로고    scopus 로고
    • Evigan: A hidden variable model for integrating gene evidence for eukaryotic gene prediction
    • Liu, Q., Mackey, A. J., Roos, D. S. & Pereira, F. C. Evigan: a hidden variable model for integrating gene evidence for eukaryotic gene prediction. Bioinformatics 24, 597-605 (2008).
    • (2008) Bioinformatics , vol.24 , pp. 597-605
    • Liu, Q.1    Mackey, A.J.2    Roos, D.S.3    Pereira, F.C.4
  • 82
    • 80053509427 scopus 로고    scopus 로고
    • Approaches to fungal genome annotation
    • This paper provides an excellent description of the process used by the Broad Institute for fungal annotation. It is also a good resource for those seeking to learn more about PASA; for more information about PASA, see reference 56
    • Haas, B. J., Zeng, Q., Pearson, M. D., Cuomo, C. A. &Wortman, J. R. Approaches to fungal genome annotation. Mycology 2, 118-141 (2011). This paper provides an excellent description of the process used by the Broad Institute for fungal annotation. It is also a good resource for those seeking to learn more about PASA; for more information about PASA, see reference 56.
    • (2011) Mycology , vol.2 , pp. 118-141
    • Haas, B.J.1    Zeng, Q.2    Pearson, M.D.3    Cuomo, C.A.4    Wortman, J.R.5
  • 83
    • 84055178433 scopus 로고    scopus 로고
    • MAKER2: An annotation pipeline and genome-database management tool for second-generation genome projects
    • This study describes the database management and annotation quality-control tools for the MAKER2 genome annotation pipeline. It also explains many of the challenges that are associated with annotating novel genomes and how to overcome them
    • Holt, C. & Yandell, M. MAKER2: an annotation pipeline and genome-database management tool for second-generation genome projects. BMC Bioinformatics 12, 491 (2011). This study describes the database management and annotation quality-control tools for the MAKER2 genome annotation pipeline. It also explains many of the challenges that are associated with annotating novel genomes and how to overcome them.
    • (2011) BMC Bioinformatics , vol.12 , pp. 491
    • Holt, C.1    Yandell, M.2
  • 84
    • 0023989064 scopus 로고
    • Improved tools for biological sequence comparison
    • Pearson, W. R. & Lipman, D. J. Improved tools for biological sequence comparison. Proc. Natl Acad. Sci. USA 85, 2444-2448 (1988).
    • (1988) Proc. Natl Acad. Sci. USA , vol.85 , pp. 2444-2448
    • Pearson, W.R.1    Lipman, D.J.2
  • 85
    • 22044443709 scopus 로고    scopus 로고
    • The Sequence Ontology: A tool for the unification of genome annotations
    • Eilbeck, K. et al. The Sequence Ontology: a tool for the unification of genome annotations. Genome Biol. 6, R44 (2005).
    • (2005) Genome Biol. , vol.6
    • Eilbeck, K.1
  • 88
    • 18644368714 scopus 로고    scopus 로고
    • The Bioperl toolkit: Perl modules for the life sciences
    • Stajich, J. E. et al. The Bioperl toolkit: Perl modules for the life sciences. Genome Res. 12, 1611-1618 (2002).
    • (2002) Genome Res. , vol.12 , pp. 1611-1618
    • Stajich, J.E.1
  • 90
    • 80054853710 scopus 로고    scopus 로고
    • Solving the problem: Genome annotation standards before the data deluge
    • Klimke, W. et al. Solving the problem: genome annotation standards before the data deluge. Stand. Genomic Sci. 5, 168-193 (2011).
    • (2011) Stand. Genomic Sci. , vol.5 , pp. 168-193
    • Klimke, W.1
  • 91
    • 79952143815 scopus 로고    scopus 로고
    • Towards viral genome annotation standards, report from the 2010 NCBI annotation workshop
    • Brister, J. R. et al. Towards viral genome annotation standards, report from the 2010 NCBI annotation workshop. Viruses 2, 2258-2268 (2010).
    • (2010) Viruses , vol.2 , pp. 2258-2268
    • Brister, J.R.1
  • 92
    • 83755162768 scopus 로고    scopus 로고
    • Meeting report: A workshop on best practices in genome annotation
    • Madupu, R. et al. Meeting report: a workshop on best practices in genome annotation. Database 2010, baq001 (2010).
    • (2010) Database , vol.2010
    • Madupu, R.1
  • 93
    • 36549003965 scopus 로고    scopus 로고
    • InterPro and InterProScan: Tools for protein sequence classification and comparison
    • Mulder, N. & Apweiler, R. InterPro and InterProScan: tools for protein sequence classification and comparison. Methods Mol. Biol. 396, 59-70 (2007).
    • (2007) Methods Mol. Biol. , vol.396 , pp. 59-70
    • Mulder, N.1    Apweiler, R.2
  • 94
    • 75549090603 scopus 로고    scopus 로고
    • The Pfam protein families database
    • Finn, R. D. et al. The Pfam protein families database. Nucleic Acids Res. 38, D211-D222 (2010).
    • (2010) Nucleic Acids Res. , vol.38
    • Finn, R.D.1
  • 96
    • 62549098614 scopus 로고    scopus 로고
    • Quantitative measures for the management and comparison of annotated genomes
    • This paper describes a number of annotation quality-control measures, including annotation edit distance (AED). It also provides some interesting meta-analyses describing the impact of curation efforts on the gene annotations of several model organism databases over a period of several years
    • Eilbeck, K., Moore, B., Holt, C. & Yandell, M. Quantitative measures for the management and comparison of annotated genomes. BMC Bioinformatics 10, 67 (2009). This paper describes a number of annotation quality-control measures, including annotation edit distance (AED). It also provides some interesting meta-analyses describing the impact of curation efforts on the gene annotations of several model organism databases over a period of several years.
    • (2009) BMC Bioinformatics , vol.10 , pp. 67
    • Eilbeck, K.1    Moore, B.2    Holt, C.3    Yandell, M.4
  • 97
    • 0012306021 scopus 로고    scopus 로고
    • Apollo: A sequence annotation editor
    • research0082
    • Lewis, S. E. et al. Apollo: a sequence annotation editor. Genome Biol. 3, research0082 (2002).
    • (2002) Genome Biol. , vol.3
    • Lewis, S.E.1
  • 98
    • 84872262557 scopus 로고    scopus 로고
    • version 1.0.31. online
    • Engels, R. Argo Genome Browser version 1.0.31. Broad Institute [online], http://www.broadinstitute.org/annotation/argo (2010).
    • (2010) Argo Genome Browser
    • Engels, R.1
  • 99
    • 0033635022 scopus 로고    scopus 로고
    • Artemis: Sequence visualization and annotation
    • Rutherford, K. et al. Artemis: sequence visualization and annotation. Bioinformatics 16, 944-945 (2000).
    • (2000) Bioinformatics , vol.16 , pp. 944-945
    • Rutherford, K.1
  • 100
    • 0034126849 scopus 로고    scopus 로고
    • Fly meets shotgun: Shotgun wins
    • Hartl, D. L. Fly meets shotgun: shotgun wins. Nature Genet. 24, 327-328 (2000).
    • (2000) Nature Genet. , vol.24 , pp. 327-328
    • Hartl, D.L.1
  • 101
    • 84859908037 scopus 로고    scopus 로고
    • online, This page explains how to use a suite of programs to set up a local Blast server for your local database
    • Desk, B. H. Introduction to the standalone WWW Blast server. National Center for Biotechnology Information [online], http://www.ncbi.nlm.nih.gov/ blast/docs/wwwblast.html (2002). This page explains how to use a suite of programs to set up a local Blast server for your local database.
    • (2002) Introduction to the Standalone WWW Blast Server
    • Desk, B.H.1
  • 102
    • 18644378331 scopus 로고    scopus 로고
    • The generic genome browser: A building block for a model organism system database
    • Stein, L. D. et al. The generic genome browser: a building block for a model organism system database. Genome Res. 12, 1599-1610 (2002).
    • (2002) Genome Res. , vol.12 , pp. 1599-1610
    • Stein, L.D.1
  • 103
    • 78651276632 scopus 로고    scopus 로고
    • Hymenoptera Genome Database: Integrated community resources for insect species of the order Hymenoptera
    • Munoz-Torres, M. C. et al. Hymenoptera Genome Database: integrated community resources for insect species of the order Hymenoptera. Nucleic Acids Res. 39, D658-D662 (2011).
    • (2011) Nucleic Acids Res. , vol.39
    • Munoz-Torres, M.C.1
  • 104
    • 79954986915 scopus 로고    scopus 로고
    • Draft genome of the globally widespread and invasive Argentine ant (Linepithema humile)
    • Smith, C. D. et al. Draft genome of the globally widespread and invasive Argentine ant (Linepithema humile). Proc. Natl Acad. Sci. USA 108, 5673-5678 (2011).
    • (2011) Proc. Natl Acad. Sci. USA , vol.108 , pp. 5673-5678
    • Smith, C.D.1
  • 105
    • 79952270451 scopus 로고    scopus 로고
    • The genome sequence of the leaf-cutter ant Atta cephalotes reveals insights into its obligate symbiotic lifestyle
    • Suen, G. et al. The genome sequence of the leaf-cutter ant Atta cephalotes reveals insights into its obligate symbiotic lifestyle. PLoS Genet. 7, e1002007 (2011).
    • (2011) PLoS Genet. , vol.7
    • Suen, G.1
  • 106
    • 80051559742 scopus 로고    scopus 로고
    • The genome of the leaf-cutting ant Acromyrmex echinatior suggests key adaptations to advanced social life and fungus farming
    • Nygaard, S. et al. The genome of the leaf-cutting ant Acromyrmex echinatior suggests key adaptations to advanced social life and fungus farming. Genome Res. 21, 1339-1348 (2011).
    • (2011) Genome Res. , vol.21 , pp. 1339-1348
    • Nygaard, S.1
  • 107
    • 2442707676 scopus 로고    scopus 로고
    • The Ensembl automatic gene annotation system
    • This paper describes the Ensembl genome annotation pipeline; although the article is now several years old, it is still a good place to start. We would recommend reading this paper and then browsing the extensive Ensembl web site for more information
    • Curwen, V. et al. The Ensembl automatic gene annotation system. Genome Res. 14, 942-950 (2004). This paper describes the Ensembl genome annotation pipeline; although the article is now several years old, it is still a good place to start. We would recommend reading this paper and then browsing the extensive Ensembl web site for more information.
    • (2004) Genome Res. , vol.14 , pp. 942-950
    • Curwen, V.1
  • 108
    • 78651270854 scopus 로고    scopus 로고
    • Gramene database in 2010: Updates and extensions
    • Youens-Clark, K. et al. Gramene database in 2010: updates and extensions. Nucleic Acids Res. 39, D1085-D1094 (2011).
    • (2011) Nucleic Acids Res. , vol.39
    • Youens-Clark, K.1
  • 109
    • 38549166729 scopus 로고    scopus 로고
    • PlantGDB: A resource for comparative plant genomics
    • Duvick, J. et al. PlantGDB: a resource for comparative plant genomics. Nucleic Acids Res. 36, D959-D965 (2008).
    • (2008) Nucleic Acids Res. , vol.36
    • Duvick, J.1
  • 110
    • 84856585935 scopus 로고    scopus 로고
    • Phytozome: A comparative platform for green plant genomics
    • Goodstein, D. M. et al. Phytozome: a comparative platform for green plant genomics. Nucleic Acids Res. 40, D1178-D1186 (2012).
    • (2012) Nucleic Acids Res. , vol.40
    • Goodstein, D.M.1
  • 111
    • 58149182729 scopus 로고    scopus 로고
    • VectorBase: A data resource for invertebrate vector genomics
    • Lawson, D. et al. VectorBase: a data resource for invertebrate vector genomics. Nucleic Acids Res. 37, D583-D587 (2009).
    • (2009) Nucleic Acids Res. , vol.37
    • Lawson, D.1
  • 112
    • 33846074757 scopus 로고    scopus 로고
    • Pseudogene.org: A comprehensive database and comparison platform for pseudogene annotation
    • Karro, J. E. et al. Pseudogene.org: a comprehensive database and comparison platform for pseudogene annotation. Nucleic Acids Res. 35, D55-D60 (2007).
    • (2007) Nucleic Acids Res. , vol.35
    • Karro, J.E.1
  • 113
    • 18144417788 scopus 로고    scopus 로고
    • Integrated pseudogene annotation for human chromosome 22: Evidence for transcription
    • Zheng, D. et al. Integrated pseudogene annotation for human chromosome 22: evidence for transcription. J. Mol. Biol. 349, 27-45 (2005).
    • (2005) J. Mol. Biol. , vol.349 , pp. 27-45
    • Zheng, D.1
  • 115
    • 34250665888 scopus 로고    scopus 로고
    • RNAmmer: Consistent and rapid annotation of ribosomal RNA genes
    • Lagesen, K. et al. RNAmmer: consistent and rapid annotation of ribosomal RNA genes. Nucleic Acids Res. 35, 3100-3108 (2007).
    • (2007) Nucleic Acids Res. , vol.35 , pp. 3100-3108
    • Lagesen, K.1
  • 116
    • 21644446318 scopus 로고    scopus 로고
    • Plant DNA flow cytometry and estimation of nuclear genome size
    • Dolezel, J. & Bartos, J. Plant DNA flow cytometry and estimation of nuclear genome size. Ann. Botany 95, 99-110 (2005).
    • (2005) Ann. Botany , vol.95 , pp. 99-110
    • Dolezel, J.1    Bartos, J.2
  • 117
    • 0014625789 scopus 로고
    • Molecular characterization of the Drosophila genome
    • Laird, C. D. & McCarthy, B. J. Molecular characterization of the Drosophila genome. Genetics 63, 865-882 (1969).
    • (1969) Genetics , vol.63 , pp. 865-882
    • Laird, C.D.1    McCarthy, B.J.2
  • 118
    • 0030854739 scopus 로고    scopus 로고
    • TRNAscan-SE: A program for improved detection of transfer RNA genes in genomic sequence
    • Lowe, T. M. & Eddy, S. R. tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res. 25, 955-964 (1997).
    • (1997) Nucleic Acids Res. , vol.25 , pp. 955-964
    • Lowe, T.M.1    Eddy, S.R.2
  • 119
    • 23144460836 scopus 로고    scopus 로고
    • The tRNAscan-SE, snoscan and snoGPS web servers for the detection of tRNAs and snoRNAs
    • Schattner, P., Brooks, A. N. & Lowe, T. M. The tRNAscan-SE, snoscan and snoGPS web servers for the detection of tRNAs and snoRNAs. Nucleic Acids Res. 33, W686-W689 (2005).
    • (2005) Nucleic Acids Res. , vol.33
    • Schattner, P.1    Brooks, A.N.2    Lowe, T.M.3
  • 121
    • 2942607685 scopus 로고    scopus 로고
    • A memory-efficient dynamic programming algorithm for optimal alignment of a sequence to an RNA secondary structure
    • Eddy, S. R. A memory-efficient dynamic programming algorithm for optimal alignment of a sequence to an RNA secondary structure. BMC Bioinformatics 3, 18 (2002).
    • (2002) BMC Bioinformatics , vol.3 , pp. 18
    • Eddy, S.R.1
  • 122
    • 0036366014 scopus 로고    scopus 로고
    • Pairwise RNA structure comparison with stochastic context-free grammars
    • Holmes, I. & Rubin, G. M. Pairwise RNA structure comparison with stochastic context-free grammars. Pac. Symp. Biocomput. 7, 163-174 (2002).
    • (2002) Pac. Symp. Biocomput. , vol.7 , pp. 163-174
    • Holmes, I.1    Rubin, G.M.2
  • 123
    • 84859881859 scopus 로고    scopus 로고
    • QIAGEN [online]
    • QIAGEN. Quick-Start Protocol miRNAeasy Mini Kit. QIAGEN [online], http://www.qiagen.com/products/rnastabilizationpurification/microrna/ mirneasyminikit.aspx#Tabs=t2 (2011).
    • (2011) Quick-Start Protocol MiRNAeasy Mini Kit
  • 124
    • 29144470346 scopus 로고    scopus 로고
    • Real-time quantification of microRNAs by stem-loop RT-PCR
    • Chen, C. et al. Real-time quantification of microRNAs by stem-loop RT-PCR. Nucleic Acids Res. 33, e179 (2005).
    • (2005) Nucleic Acids Res. , vol.33
    • Chen, C.1
  • 125
    • 78049308870 scopus 로고    scopus 로고
    • Long non-coding RNAs: Guardians of development
    • van Leeuwen, S. & Mikkers, H. Long non-coding RNAs: guardians of development. Differentiation 80, 175-183 (2010).
    • (2010) Differentiation , vol.80 , pp. 175-183
    • Van Leeuwen, S.1    Mikkers, H.2
  • 126
    • 78649339069 scopus 로고    scopus 로고
    • Long noncoding RNA in genome regulation: Prospects and mechanisms
    • Hung., T. & Chang, H. Y. Long noncoding RNA in genome regulation: prospects and mechanisms. RNA Biol. 7, 582-585 (2010).
    • (2010) RNA Biol. , vol.7 , pp. 582-585
    • Hung, T.1    Chang, H.Y.2
  • 127
    • 44349159416 scopus 로고    scopus 로고
    • Pseudogene-derived small interfering RNAs regulate gene expression in mouse oocytes
    • Tam, O. H. et al. Pseudogene-derived small interfering RNAs regulate gene expression in mouse oocytes. Nature 453, 534-538 (2008).
    • (2008) Nature , vol.453 , pp. 534-538
    • Tam, O.H.1
  • 128
    • 1642473033 scopus 로고    scopus 로고
    • Comparative analysis of processed pseudogenes in the mouse and human genomes
    • Zhang, Z., Carriero, N. & Gerstein, M. Comparative analysis of processed pseudogenes in the mouse and human genomes. Trends Genet. 20, 62-67 (2004).
    • (2004) Trends Genet. , vol.20 , pp. 62-67
    • Zhang, Z.1    Carriero, N.2    Gerstein, M.3
  • 129
    • 65549111754 scopus 로고    scopus 로고
    • Infernal 1.0: Inference of RNA alignments
    • Nawrocki, E. P., Kolbe, D. L. & Eddy, S. R. Infernal 1.0: inference of RNA alignments. Bioinformatics 25, 1335-1337 (2009).
    • (2009) Bioinformatics , vol.25 , pp. 1335-1337
    • Nawrocki, E.P.1    Kolbe, D.L.2    Eddy, S.R.3
  • 130
    • 0030585734 scopus 로고    scopus 로고
    • Evaluation of gene structure prediction programs
    • This paper provides an excellent explanation of how sensitivity and specificity measures can be used to evaluate gene finder performance. This is a classic paper in the field and should be read by anyone involved in gene annotation
    • Burset, M. & Guigo, R. Evaluation of gene structure prediction programs. Genomics 34, 353-367 (1996). This paper provides an excellent explanation of how sensitivity and specificity measures can be used to evaluate gene finder performance. This is a classic paper in the field and should be read by anyone involved in gene annotation.
    • (1996) Genomics , vol.34 , pp. 353-367
    • Burset, M.1    Guigo, R.2
  • 131
    • 0033931867 scopus 로고    scopus 로고
    • Assessing the accuracy of prediction algorithms for classification: An overview
    • Baldi, P., Brunak, S., Chauvin, Y., Andersen, C. A. &Nielsen, H. Assessing the accuracy of prediction algorithms for classification: an overview. Bioinformatics 16, 412-424 (2000).
    • (2000) Bioinformatics , vol.16 , pp. 412-424
    • Baldi, P.1    Brunak, S.2    Chauvin, Y.3    Andersen, C.A.4    Nielsen, H.5
  • 132
    • 33748641351 scopus 로고    scopus 로고
    • EGASP: The human ENCODE Genome Annotation Assessment Project
    • Guigo, R. et al. EGASP: the human ENCODE Genome Annotation Assessment Project. Genome Biol. 7 (Suppl. 1), 1-31 (2006).
    • (2006) Genome Biol. , vol.7 , Issue.SUPPL. 1 , pp. 1-31
    • Guigo, R.1
  • 133
    • 70350708134 scopus 로고    scopus 로고
    • MGene: Accurate SVM-based gene finding with an application to nematode genomes
    • Schweikert, G. et al. mGene: accurate SVM-based gene finding with an application to nematode genomes. Genome Res. 19, 2133-2143 (2009).
    • (2009) Genome Res. , vol.19 , pp. 2133-2143
    • Schweikert, G.1
  • 135
    • 0035002015 scopus 로고    scopus 로고
    • Computational inference of homologous gene structures in the human genome
    • Yeh, R. F., Lim, L. P. & Burge, C. B. Computational inference of homologous gene structures in the human genome. Genome Res. 11, 803-816 (2001).
    • (2001) Genome Res. , vol.11 , pp. 803-816
    • Yeh, R.F.1    Lim, L.P.2    Burge, C.B.3
  • 136
    • 34548390530 scopus 로고    scopus 로고
    • Conrad: Gene prediction using conditional random fields
    • DeCaprio, D. et al. Conrad: gene prediction using conditional random fields. Genome Res. 17, 1389-1398 (2007).
    • (2007) Genome Res. , vol.17 , pp. 1389-1398
    • DeCaprio, D.1
  • 137
    • 40449115745 scopus 로고    scopus 로고
    • CONTRAST: A discriminative, phylogeny-free approach to multiple informant de novo gene prediction
    • Gross, S. S., Do, C. B., Sirota, M. & Batzoglou, S. CONTRAST: a discriminative, phylogeny-free approach to multiple informant de novo gene prediction. Genome Biol. 8, R269 (2007).
    • (2007) Genome Biol. , vol.8
    • Gross, S.S.1    Do, C.B.2    Sirota, M.3    Batzoglou, S.4
  • 138
    • 34047200354 scopus 로고    scopus 로고
    • Global discriminative learning for higher-accuracy computational gene prediction
    • Bernal, A., Crammer, K., Hatzigeorgiou, A. &Pereira, F. Global discriminative learning for higher-accuracy computational gene prediction. PLoS Comput. Biol. 3, e54 (2007).
    • (2007) PLoS Comput. Biol. , vol.3
    • Bernal, A.1    Crammer, K.2    Hatzigeorgiou, A.3    Pereira, F.4
  • 139
    • 0034129194 scopus 로고    scopus 로고
    • Optimal spliced alignment of homologous cDNA to a genomic DNA template
    • Usuka, J., Zhu, W. & Brendel, V. Optimal spliced alignment of homologous cDNA to a genomic DNA template. Bioinformatics 16, 203-211 (2000).
    • (2000) Bioinformatics , vol.16 , pp. 203-211
    • Usuka, J.1    Zhu, W.2    Brendel, V.3
  • 140
    • 84859906777 scopus 로고    scopus 로고
    • online
    • Kiryutin, B. ProSplign. National Center for Biotechnology Information [online], http://www.ncbi.nlm.nih.gov/sutils/static/prosplign/prosplign.html (2011).
    • (2011) ProSplign
    • Kiryutin, B.1
  • 141
    • 78649345104 scopus 로고    scopus 로고
    • MapSplice: Accurate mapping of RNAseq reads for splice junction discovery
    • Wang, K. et al. MapSplice: accurate mapping of RNAseq reads for splice junction discovery. Nucleic Acids Res. 38, e178 (2010).
    • (2010) Nucleic Acids Res. , vol.38
    • Wang, K.1
  • 142
    • 84859897748 scopus 로고    scopus 로고
    • (ed. McEntyre, J. &Ostell, J.) (National Center for Biotechnology Information)
    • Kitts, P. in The NCBI Handbook (ed. McEntyre, J. &Ostell, J.) (National Center for Biotechnology Information, 2003).
    • (2003) The NCBI Handbook
    • Kitts, P.1
  • 143
    • 78651271733 scopus 로고    scopus 로고
    • Integrative genomics viewer
    • Robinson, J. T. et al. Integrative genomics viewer. Nature Biotech. 29, 24-26 (2011).
    • (2011) Nature Biotech. , vol.29 , pp. 24-26
    • Robinson, J.T.1


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