메뉴 건너뛰기




Volumn 859, Issue , 2012, Pages 105-114

Methods and software in NGS for TE analysis

Author keywords

Interspersion; NGS; Repeats; Retrotransposon; Transposon

Indexed keywords

SMALL INTERFERING RNA; TRANSCRIPTOME;

EID: 84860173551     PISSN: 10643745     EISSN: None     Source Type: Book Series    
DOI: 10.1007/978-1-61779-603-6_6     Document Type: Article
Times cited : (6)

References (22)
  • 1
    • 56549090030 scopus 로고    scopus 로고
    • Low-pass shotgun sequencing of the barley genome facilitates rapid identifi cation of genes, conserved noncoding sequences and novel repeats
    • Wicker T, et al. (2008) Low-pass shotgun sequencing of the barley genome facilitates rapid identifi cation of genes, conserved noncoding sequences and novel repeats. BMC Genomics 9:518
    • (2008) BMC Genomics. , vol.9 , pp. 518
    • Wicker, T.1
  • 2
    • 56549086632 scopus 로고    scopus 로고
    • A new method to compute K-mer frequencies and its application to annotate large repetitive plant genomes
    • Kurtz S, et al. (2008) A new method to compute K-mer frequencies and its application to annotate large repetitive plant genomes. BMC Genomics 9:517
    • (2008) BMC Genomics. , vol.9 , pp. 517
    • Kurtz, S.1
  • 3
    • 79952592810 scopus 로고    scopus 로고
    • A fast, lockfree approach for effi cient parallel counting of occurrences of k-mers
    • Marcais G, Kingsford C (2011) A fast, lockfree approach for effi cient parallel counting of occurrences of k-mers. Bioinformatics 27: 764-770
    • (2011) Bioinformatics , vol.27 , pp. 764-770
    • Marcais, G.1    Kingsford, C.2
  • 4
    • 79952178131 scopus 로고    scopus 로고
    • High-quality draft assemblies of mammalian genomes from massively parallel sequence data
    • Gnerre S, et al. (2011) High-quality draft assemblies of mammalian genomes from massively parallel sequence data. Proc Natl Acad Sci USA 108:1513-1518
    • (2011) Proc. Natl. Acad. Sci. USA , vol.108 , pp. 1513-1518
    • Gnerre, S.1
  • 5
    • 79251632958 scopus 로고    scopus 로고
    • The genome of theobroma cacao
    • Argout X, et al. (2010) The genome of Theobroma cacao. Nat Genet 43:101-108
    • (2010) Nat. Genet. , vol.43 , pp. 101-108
    • Argout, X.1
  • 6
    • 50649089207 scopus 로고    scopus 로고
    • RNA-seq: An assessment of technical reproducibility and comparison with gene expression arrays
    • Marioni JC, et al. (2008) RNA-seq: An assessment of technical reproducibility and comparison with gene expression arrays. Genome Res 18:1509-1517
    • (2008) Genome Res. , vol.18 , pp. 1509-1517
    • Marioni, J.C.1
  • 7
    • 78650630076 scopus 로고    scopus 로고
    • Evolutionary dynamics of transposable elements in a small RNA world
    • Blumenstiel JP (2011) Evolutionary dynamics of transposable elements in a small RNA world. Trends in Genetics 27:23-31
    • (2011) Trends in Genetics. , vol.27 , pp. 23-31
    • Blumenstiel, J.P.1
  • 8
    • 79955028255 scopus 로고    scopus 로고
    • Transpositional landscape of rice genome revealed by Paired-End Mapping of high-throughput resequencing data
    • doi: 10.1111/j.1365-313X.2011.04492.x . [Epub ahead of print]
    • Sabot F, et al. (2011) Transpositional landscape of rice genome revealed by Paired-End Mapping of high-throughput resequencing data. Plant J doi: 10.1111/j.1365-313X.2011.04492.x . [Epub ahead of print]
    • (2011) Plant. J.
    • Sabot, F.1
  • 9
    • 70349278339 scopus 로고    scopus 로고
    • Selective epigenetic control of retrotransposition in arabidopsis
    • Mirouze M, et al. (2009) Selective epigenetic control of retrotransposition in Arabidopsis. Nature 461:427-430
    • (2009) Nature. , vol.461 , pp. 427-430
    • Mirouze, M.1
  • 10
    • 79953710031 scopus 로고    scopus 로고
    • T-lex: A program for fast and accurate assessment of transposable element presence using next-generation sequencing data
    • Fiston-Lavier A, et al. (2010) T-lex: a program for fast and accurate assessment of transposable element presence using next-generation sequencing data. Nucleic Acids Res 39:e36
    • (2010) Nucleic. Acids. Res. , vol.39
    • Fiston-Lavier, A.1
  • 11
    • 67649884743 scopus 로고    scopus 로고
    • Fast and accurate short read alignment with burrows-wheeler transform
    • Li H, Durbin R (2009) Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25:1754-1760
    • (2009) Bioinformatics , vol.25 , pp. 1754-1760
    • Li, H.1    Durbin, R.2
  • 12
    • 62349130698 scopus 로고    scopus 로고
    • Ultrafast and emory-effi cient alignment of short DNA sequences to the human genome
    • Langmead B, et al. (2009) Ultrafast and emory-effi cient alignment of short DNA sequences to the human genome. Genome Biol 10:R25
    • (2009) Genome. Biol. , vol.10
    • Langmead, B.1
  • 13
    • 55549097836 scopus 로고    scopus 로고
    • Mapping short DNA sequencing reads and calling variants using mapping quality scores
    • Li H, Ruan J, Durbin R (2008) Mapping short DNA sequencing reads and calling variants using mapping quality scores. Genome Res 18:1851-1858
    • (2008) Genome Res. , vol.18 , pp. 1851-1858
    • Li, H.1    Ruan, J.2    Durbin, R.3
  • 14
    • 67650711615 scopus 로고    scopus 로고
    • SOAP2: An improved ultrafast tool for short read alignment
    • Li R, et al. (2009) SOAP2: an improved ultrafast tool for short read alignment. Bioinformatics 25:1966-1967
    • (2009) Bioinformatics , vol.25 , pp. 1966-1967
    • Li, R.1
  • 15
    • 24044447664 scopus 로고    scopus 로고
    • Automated generation of heuristics for biological sequence comparison
    • Slater G. Birney E. 2005 Automated generation of heuristics for biological sequence comparison BMC Bioinformatics 6 31
    • (2005) BMC Bioinformatics , vol.6 , pp. 31
    • Slater, G.1    Birney, E.2
  • 16
    • 77952123055 scopus 로고    scopus 로고
    • Transcript assembly and quantifi cation by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation
    • Slater G, Birney E (2005) Automated generation of heuristics for biological sequence comparison. BMC Bioinformatics 6:31 16. Trapnell C, et al. (2010) Transcript assembly and quantifi cation by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat Biotech 28: 511-515
    • (2010) Nat. Biotech. , vol.28 , pp. 511-515
    • Trapnell, C.1
  • 17
    • 65449136284 scopus 로고    scopus 로고
    • TopHat: Discovering splice junctions with RNA-Seq
    • Trapnell C, Pachter L, Salzberg SL (2009) TopHat: discovering splice junctions with RNA-Seq. Bioinformatics 25:1105-1111
    • (2009) Bioinformatics , vol.25 , pp. 1105-1111
    • Trapnell, C.1    Pachter, L.2    Salzberg, S.L.3
  • 18
    • 77954139210 scopus 로고    scopus 로고
    • Incorporating sequence quality data into alignment improves DNA read mapping
    • Frith MC, Wan R, Horton P (2010) Incorporating sequence quality data into alignment improves DNA read mapping. Nucl. Acids Res 38:e100
    • (2010) Nucl. Acids. Res. , vol.38
    • Frith, M.C.1    Wan, R.2    Horton, P.3
  • 19
    • 43149115851 scopus 로고    scopus 로고
    • Velvet: Algorithms for de novo short read assembly using de Bruijn graphs
    • DOI 10.1101/gr.074492.107
    • Zerbino, D.R., Birney, E., 2008. Velvet: Algorithms for de novo short read assembly using de Bruijn graphs. Genome Research 18, 821-829 (Pubitemid 351645072)
    • (2008) Genome Research , vol.18 , Issue.5 , pp. 821-829
    • Zerbino, D.R.1    Birney, E.2
  • 20
    • 66449136667 scopus 로고    scopus 로고
    • ABySS: A parallel assembler for short read sequence data
    • Simpson JT, et al. (2009) ABySS: A parallel assembler for short read sequence data. Genome Res 19:1117-1123
    • (2009) Genome Res. , vol.19 , pp. 1117-1123
    • Simpson, J.T.1
  • 21
    • 78049346632 scopus 로고    scopus 로고
    • De novo assembly and analysis of RNA-seq data
    • Robertson G, et al. (2010) De novo assembly and analysis of RNA-seq data. Nat Meth 7:909-912
    • (2010) Nat. Meth. , vol.7 , pp. 909-912
    • Robertson, G.1
  • 22
    • 44849114374 scopus 로고    scopus 로고
    • Discovery and assembly of repeat family pseudomolecules from sparse genomic sequence data using the assisted automated assembler of repeat families (aaarf) algorithm
    • DeBarry J, Liu R, Bennetzen J (2008) Discovery and assembly of repeat family pseudomolecules from sparse genomic sequence data using the Assisted Automated Assembler of Repeat Families (AAARF) algorithm. BMC Bioinformatics 9:235
    • (2008) BMC Bioinformatics , vol.9 , pp. 235
    • DeBarry, J.1    Liu, R.2    Bennetzen, J.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.