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Volumn 5, Issue 1, 2016, Pages

Improved hybrid de novo genome assembly of domesticated apple (Malus x domestica)

Author keywords

Apple; Illumina sequencing; Malus x domestica; PacBio sequencing

Indexed keywords

CONTIG; UNTRANSLATED RNA;

EID: 85007305380     PISSN: None     EISSN: 2047217X     Source Type: Journal    
DOI: 10.1186/s13742-016-0139-0     Document Type: Article
Times cited : (54)

References (24)
  • 1
    • 84865591846 scopus 로고    scopus 로고
    • A tale of three next generation sequencing platforms: comparison of Ion Torrent, Pacific Biosciences and Illumina MiSeq sequencers
    • Quail MA, Smith M, Coupland P, Otto TD, Harris SR, Connor TR, et al. A tale of three next generation sequencing platforms: comparison of Ion Torrent, Pacific Biosciences and Illumina MiSeq sequencers. BMC Genomics. 2012;13:341.
    • (2012) BMC Genomics , vol.13 , pp. 341
    • Quail, M.A.1    Smith, M.2    Coupland, P.3    Otto, T.D.4    Harris, S.R.5    Connor, T.R.6
  • 2
    • 84942887758 scopus 로고    scopus 로고
    • SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler
    • Luo R, Liu B, Xie Y, Li Z, Huang W, Yuan J, et al. SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler. Gigascience. 2012;1:18-24.
    • (2012) Gigascience , vol.1 , pp. 18-24
    • Luo, R.1    Liu, B.2    Xie, Y.3    Li, Z.4    Huang, W.5    Yuan, J.6
  • 3
    • 58149234737 scopus 로고    scopus 로고
    • Real-time DNA sequencing from single polymerase molecules
    • Eid J, Fehr A, Gray J, Luong K, Lyle J, Otto G, et al. Real-time DNA sequencing from single polymerase molecules. Science. 2009;323:133-8.
    • (2009) Science , vol.323 , pp. 133-138
    • Eid, J.1    Fehr, A.2    Gray, J.3    Luong, K.4    Lyle, J.5    Otto, G.6
  • 4
    • 79952592810 scopus 로고    scopus 로고
    • A fast, lock-free approach for efficient parallel counting of occurrences of k-mers
    • Marçais G, Kingsford C. A fast, lock-free approach for efficient parallel counting of occurrences of k-mers. Bioinformatics. 2011;27:764-70.
    • (2011) Bioinformatics , vol.27 , pp. 764-770
    • Marçais, G.1    Kingsford, C.2
  • 7
    • 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. 2007;23:1061-7.
    • (2007) Bioinformatics , vol.23 , pp. 1061-1067
    • Parra, G.1    Bradnam, K.2    Korf, I.3
  • 8
    • 0033555906 scopus 로고    scopus 로고
    • Tandem repeats finder: a program to analyze DNA sequences
    • Benson G. Tandem repeats finder: a program to analyze DNA sequences. Nucleic Acids Res. 1999;27:573-80.
    • (1999) Nucleic Acids Res , vol.27 , pp. 573-580
    • Benson, G.1
  • 9
    • 63049126614 scopus 로고    scopus 로고
    • Using RepeatMasker to identify repetitive elements in genomic sequences
    • Tarailo-Graovac M, Chen N. Using RepeatMasker to identify repetitive elements in genomic sequences. Curr Protoc Bioinformatics. 2009;3:4-14.
    • (2009) Curr Protoc Bioinformatics , vol.3 , pp. 4-14
    • Tarailo-Graovac, M.1    Chen, N.2
  • 12
    • 34547592867 scopus 로고    scopus 로고
    • LTR_FINDER: an efficient tool for the prediction of full-length LTR retrotransposons
    • Xu Z, Wang H. LTR_FINDER: an efficient tool for the prediction of full-length LTR retrotransposons. Nucleic Acids Res. 2007;35 Suppl 2:W265-8.
    • (2007) Nucleic Acids Res , vol.35 , pp. W265-W268
    • Xu, Z.1    Wang, H.2
  • 14
    • 84900037594 scopus 로고    scopus 로고
    • Computational systems biology methods in molecular biology, chemistry biology, molecular biomedicine, and biopharmacy
    • Cai Y, Gonzalez JV, Liu Z, Huang T. Computational systems biology methods in molecular biology, chemistry biology, molecular biomedicine, and biopharmacy. Biomed Res Int. 2014;2014:746814.
    • (2014) Biomed Res Int , vol.2014
    • Cai, Y.1    Gonzalez, J.V.2    Liu, Z.3    Huang, T.4
  • 15
    • 8844252293 scopus 로고    scopus 로고
    • TigrScan and GlimmerHMM: two open source ab initio eukaryotic gene-finders
    • Majoros WH, Pertea M, Salzberg SL. TigrScan and GlimmerHMM: two open source ab initio eukaryotic gene-finders. Bioinformatics. 2004;20:2878-9.
    • (2004) Bioinformatics , vol.20 , pp. 2878-2879
    • Majoros, W.H.1    Pertea, M.2    Salzberg, S.L.3
  • 16
    • 2942544417 scopus 로고    scopus 로고
    • Gene finding in novel genomes
    • Korf I. Gene finding in novel genomes. BMC Bioinformatics. 2004;5:59.
    • (2004) BMC Bioinformatics , vol.5 , pp. 59
    • Korf, I.1
  • 18
    • 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. 2000;10:547-8.
    • (2000) Genome Res , vol.10 , pp. 547-548
    • Birney, E.1    Durbin, R.2
  • 19
    • 84859885816 scopus 로고    scopus 로고
    • Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks
    • Trapnell C, Roberts A, GoffL, Pertea G, Kim D, Kelley DR, et al. Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks. Nature Protoc. 2012;7:562-78.
    • (2012) Nature Protoc , vol.7 , pp. 562-578
    • Trapnell, C.1    Roberts, A.2    Goff, L.3    Pertea, G.4    Kim, D.5    Kelley, D.R.6
  • 20
    • 42949086676 scopus 로고    scopus 로고
    • Automated eukaryotic gene structure annotation using EVidenceModeler and the Program to Assemble Spliced Alignments
    • Haas BJ, Salzberg SL, Zhu W, Pertea M, Eallen J, Orvis J, et al. Automated eukaryotic gene structure annotation using EVidenceModeler and the Program to Assemble Spliced Alignments. Genome Biol. 2008;9:R7.
    • (2008) Genome Biol , vol.9 , pp. R7
    • Haas, B.J.1    Salzberg, S.L.2    Zhu, W.3    Pertea, M.4    Eallen, J.5    Orvis, J.6
  • 21
    • 0030854739 scopus 로고    scopus 로고
    • tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence
    • Lowe TM, Eddy SR. tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res. 1997;25:955-64.
    • (1997) Nucleic Acids Res , vol.25 , pp. 955-964
    • Lowe, T.M.1    Eddy, S.R.2
  • 23
    • 84890037468 scopus 로고    scopus 로고
    • Infernal 1.1: 100-fold faster RNA homology searches
    • Nawrocki EP, Eddy SR. Infernal 1.1: 100-fold faster RNA homology searches. Bioinformatics. 2013;29:2933-5.
    • (2013) Bioinformatics , vol.29 , pp. 2933-2935
    • Nawrocki, E.P.1    Eddy, S.R.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.