메뉴 건너뛰기




Volumn 7, Issue 12, 2012, Pages

A Comprehensive Evaluation of Alignment Algorithms in the Context of RNA-Seq

Author keywords

[No Author keywords available]

Indexed keywords

RNA; TRANSCRIPTOME;

EID: 84871593783     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0052403     Document Type: Article
Times cited : (58)

References (21)
  • 1
    • 57749195712 scopus 로고    scopus 로고
    • RNA-Seq: a revolutionary tool for transcriptomics
    • Wang Z, Gerstein M, Snyder M, (2009) RNA-Seq: a revolutionary tool for transcriptomics. Nature Reviews Genetics 10: 57-63.
    • (2009) Nature Reviews Genetics , vol.10 , pp. 57-63
    • Wang, Z.1    Gerstein, M.2    Snyder, M.3
  • 3
    • 77955443472 scopus 로고    scopus 로고
    • Detection of splice junctions from paired-end RNA-seq data by SpliceMap
    • Au KF, Jiang H, Lin L, Xing Y, Wong WH, (2010) Detection of splice junctions from paired-end RNA-seq data by SpliceMap. Nucleic Acids Res 38: 4570-4578.
    • (2010) Nucleic Acids Res , vol.38 , pp. 4570-4578
    • Au, K.F.1    Jiang, H.2    Lin, L.3    Xing, Y.4    Wong, W.H.5
  • 4
    • 78649345104 scopus 로고    scopus 로고
    • MapSplice: accurate mapping of RNA-seq reads for splice junction discovery
    • Wang K, et al. (2010) MapSplice: accurate mapping of RNA-seq reads for splice junction discovery. Nucleic Acids Research 38: e178.
    • (2010) Nucleic Acids Research , vol.38
    • Wang, K.1
  • 5
    • 80052745094 scopus 로고    scopus 로고
    • Comparative analysis of RNA-Seq alignment algorithms and the RNA-Seq unified mapper (RUM)
    • Grant GR, Farkas MH, Pizarro AD, Lahens NF, Schug J, et al. (2011) Comparative analysis of RNA-Seq alignment algorithms and the RNA-Seq unified mapper (RUM). Bioinformatics 27: 2518-2528.
    • (2011) Bioinformatics , vol.27 , pp. 2518-2528
    • Grant, G.R.1    Farkas, M.H.2    Pizarro, A.D.3    Lahens, N.F.4    Schug, J.5
  • 7
    • 84867882225 scopus 로고    scopus 로고
    • A context-based approach to identify the most likely mapping for RNA-seq experiments
    • Bonfert T, Csaba G, Zimmer R, Friedel CC (2012) A context-based approach to identify the most likely mapping for RNA-seq experiments. BMC Bioinformatics (Suppl 6): S9.
    • (2012) BMC Bioinformatics , Issue.SUPPL. 6
    • Bonfert, T.1    Csaba, G.2    Zimmer, R.3    Friedel, C.C.4
  • 8
    • 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 Research 18: 1851-1858.
    • (2008) Genome Research , vol.18 , pp. 1851-1858
    • Li, H.1    Ruan, J.2    Durbin, R.3
  • 9
    • 62349130698 scopus 로고    scopus 로고
    • Ultrafast and memory-efficient alignment of short DNA sequences to the human genome
    • Langmead B, Trapnell C, Pop M, Salzberg SL, (2009) Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biology 10: R25.
    • (2009) Genome Biology , vol.10
    • Langmead, B.1    Trapnell, C.2    Pop, M.3    Salzberg, S.L.4
  • 10
    • 80053978849 scopus 로고    scopus 로고
    • Comparative analysis of algorithms for next-generation sequencing read alignment
    • Ruffalo M, Laframboise T, Koyutrk M, (2011) Comparative analysis of algorithms for next-generation sequencing read alignment. Bioinformatics 27: 2790-2796.
    • (2011) Bioinformatics , vol.27 , pp. 2790-2796
    • Ruffalo, M.1    Laframboise, T.2    Koyutrk, M.3
  • 11
    • 70450177746 scopus 로고    scopus 로고
    • BFAST: an alignment tool for large scale genome resequencing
    • Homer N, Merriman B, Nelson SF, (2009) BFAST: an alignment tool for large scale genome resequencing. PLoS ONE 4: e7767.
    • (2009) PLoS ONE , vol.4
    • Homer, N.1    Merriman, B.2    Nelson, S.F.3
  • 12
    • 75249084378 scopus 로고    scopus 로고
    • The GNUMAP algorithm: unbiased probabilistic mapping of oligonucleotides from next-generation sequencing
    • Clement NL, et al. (2010) The GNUMAP algorithm: unbiased probabilistic mapping of oligonucleotides from next-generation sequencing. Bioinformatics 26: 38-45.
    • (2010) Bioinformatics , vol.26 , pp. 38-45
    • Clement, N.L.1
  • 14
    • 70350697851 scopus 로고    scopus 로고
    • Updates to the RMAP short-read mapping software
    • Smith AD, et al. (2009) Updates to the RMAP short-read mapping software. Bioinformatics (Oxford, England) 25: 2841-2842.
    • (2009) Bioinformatics (Oxford, England) , vol.25 , pp. 2841-2842
    • Smith, A.D.1
  • 16
    • 2942538300 scopus 로고    scopus 로고
    • Versatile and open software for comparing large genomes
    • Kurtz S, et al. (2004) Versatile and open software for comparing large genomes. Genome Biology 5: R12.
    • (2004) Genome Biology , vol.5
    • Kurtz, S.1
  • 18
    • 0003573193 scopus 로고
    • A block-sorting lossless data compression algorithm
    • Digital Equipment Corporation, Palo Alto, CA
    • Burrows M, Wheeler D (1994) A block-sorting lossless data compression algorithm. Technical Report 124, Digital Equipment Corporation, Palo Alto, CA.
    • (1994) Technical Report 124
    • Burrows, M.1    Wheeler, D.2
  • 19
    • 77949587649 scopus 로고    scopus 로고
    • Fast and accurate long-read alignment with Burrows-Wheeler transform
    • Li H, Durbin R, (2010) Fast and accurate long-read alignment with Burrows-Wheeler transform. Bioinformatics (Oxford, England) 26: 589-595.
    • (2010) Bioinformatics (Oxford, England) , vol.26 , pp. 589-595
    • Li, H.1    Durbin, R.2
  • 20
    • 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
  • 21
    • 84859210032 scopus 로고    scopus 로고
    • Fast gapped-read alignment with bowtie 2
    • Langmead B, Salzberg SL, (2012) Fast gapped-read alignment with bowtie 2. Nat Methods 9: 357-359.
    • (2012) Nat Methods , vol.9 , pp. 357-359
    • Langmead, B.1    Salzberg, S.L.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.