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Volumn 1038, Issue , 2013, Pages 113-135

Profiling short tandem repeats from short reads

Author keywords

lobSTR; Microsatellites; Personal genomes; Short tandem repeats; Variant calling; Whole genome sequencing

Indexed keywords

ARTICLE; GENOME; HIGH THROUGHPUT SEQUENCING; POPULATION GENETICS; PRIORITY JOURNAL; SHORT TANDEM REPEAT;

EID: 84881088721     PISSN: 10643745     EISSN: None     Source Type: Book Series    
DOI: 10.1007/978-1-62703-514-9_7     Document Type: Article
Times cited : (4)

References (28)
  • 1
    • 34250878426 scopus 로고    scopus 로고
    • Expandable DNA repeats and human disease
    • Mirkin SM (2007) Expandable DNA repeats and human disease. Nature 447:932
    • (2007) Nature , vol.447 , pp. 932
    • Mirkin, S.M.1
  • 2
    • 0027480960 scopus 로고
    • A novel gene containing a trinucleotide repeat that is expanded and unstable on Huntington's disease chromosomes
    • The Huntington's Disease Collaborative Research Group
    • (1993) A novel gene containing a trinucleotide repeat that is expanded and unstable on Huntington's disease chromosomes. The Huntington's Disease Collaborative Research Group. Cell 72: 971
    • (1993) Cell , vol.72 , pp. 971
  • 4
    • 78751694575 scopus 로고    scopus 로고
    • Trinucleotide repeats: Triggers for genomic disorders?
    • Kozlowski P, Sobczak K, Krzyzosiak WJ (2010) Trinucleotide repeats: Triggers for genomic disorders? Genome Med 2:29
    • (2010) Genome Med , vol.2 , pp. 29
    • Kozlowski, P.1    Sobczak, K.2    Krzyzosiak, W.J.3
  • 5
    • 0032231877 scopus 로고    scopus 로고
    • Comprehensive human genetic maps: Individual and sex-specific variation in recombination
    • Broman KW, Murray JC, Sheffield VC, White RL, Weber JL (1998) Comprehensive human genetic maps: Individual and sex-specific variation in recombination.AmJHumGenet 63:861
    • (1998) AmJHumGenet , vol.63 , pp. 861
    • Broman, K.W.1    Murray, J.C.2    Sheffield, V.C.3    White, R.L.4    Weber, J.L.5
  • 6
    • 3042775276 scopus 로고    scopus 로고
    • Forensic DNA typing by capillary electrophoresis using the ABI Prism 310 and 3100 genetic analyzers for STR analysis
    • Butler JM, Buel E, Crivellente F, McCord BR (2004) Forensic DNA typing by capillary electrophoresis using the ABI Prism 310 and 3100 genetic analyzers for STR analysis. Electrophoresis 25:1397
    • (2004) Electrophoresis , vol.25 , pp. 1397
    • Butler, J.M.1    Buel, E.2    Crivellente, F.3    McCord, B.R.4
  • 7
    • 9144274354 scopus 로고    scopus 로고
    • The effective mutation rate at Y chromosome short tandem repeats, with application to human populationdivergence time
    • Zhivotovsky LA et al (2004) The effective mutation rate at Y chromosome short tandem repeats, with application to human populationdivergence time. Am J Hum Genet 74:50
    • (2004) Am J Hum Genet , vol.74 , pp. 50
    • Zhivotovsky, L.A.1
  • 8
    • 83855165105 scopus 로고    scopus 로고
    • Repetitive DNA and next-generation sequencing: Computational challenges and solutions
    • Treangen TJ, Salzberg SL (2012) Repetitive DNA and next-generation sequencing: Computational challenges and solutions. Nat Rev Genet 13:36
    • (2012) Nat Rev Genet , vol.13 , pp. 36
    • Treangen, T.J.1    Salzberg, S.L.2
  • 9
    • 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
    • (2009) Bioinformatics , vol.25 , pp. 1754
    • Li, H.1    Durbin, R.2
  • 10
    • 77957272611 scopus 로고    scopus 로고
    • A survey of sequence alignment algorithms for next-generation sequencing
    • Li H, Homer N (2010) A survey of sequence alignment algorithms for next-generation sequencing. Brief Bioinform 11:473
    • (2010) Brief Bioinform , vol.11 , pp. 473
    • Li, H.1    Homer, N.2
  • 11
    • 84861861291 scopus 로고    scopus 로고
    • LobSTR: A short tandem repeat profiler for personal genomes
    • Gymrek M, Golan D, Rosset S, Erlich Y (2012) lobSTR: A short tandem repeat profiler for personal genomes. Genome Res 22 (6):1154-1162
    • (2012) Genome Res , vol.22 , Issue.6 , pp. 1154-1162
    • Gymrek, M.1    Golan, D.2    Rosset, S.3    Erlich, Y.4
  • 12
    • 79960405019 scopus 로고    scopus 로고
    • The variant call format and VCFtools
    • Danecek P et al (2011) The variant call format and VCFtools. Bioinformatics 27:2156
    • (2011) Bioinformatics , vol.27 , pp. 2156
    • Danecek, P.1
  • 13
    • 0033555906 scopus 로고    scopus 로고
    • Tandem repeats finder: A program to analyze DNA sequences
    • Benson G (1999) Tandem repeats finder: A program to analyze DNA sequences. Nucleic Acids Res 27:573
    • (1999) Nucleic Acids Res , vol.27 , pp. 573
    • Benson, G.1
  • 14
    • 0036079158 scopus 로고    scopus 로고
    • The human genome browser at UCSC
    • Kent WJ et al (2002) The human genome browser at UCSC. Genome Res 12:996
    • (2002) Genome Res , vol.12 , pp. 996
    • Kent, W.J.1
  • 15
    • 78651271733 scopus 로고    scopus 로고
    • Integrative genomics viewer
    • Robinson JT et al (2011) Integrative genomics viewer. Nat Biotechnol 29:24
    • (2011) Nat Biotechnol , vol.29 , pp. 24
    • Robinson, J.T.1
  • 16
    • 77951226627 scopus 로고    scopus 로고
    • The Sanger FASTQ file format for sequences with quality scores, and the Solexa/ Illumina FASTQ variants
    • Cock PJ, FieldsCJ,Goto N,HeuerML, RicePM (2010) The Sanger FASTQ file format for sequences with quality scores, and the Solexa/ Illumina FASTQ variants. Nucleic Acids Res 38:1767
    • (2010) Nucleic Acids Res , vol.38 , pp. 1767
    • Cock, P.J.1    Fields, C.J.2    Goto, N.3    Heuer, M.L.4    Rice, P.M.5
  • 17
    • 68549104404 scopus 로고    scopus 로고
    • The sequence alignment/map format and SAMtools
    • LiH et al (2009) The sequence alignment/map format and SAMtools. Bioinformatics 25:2078
    • (2009) Bioinformatics , vol.25 , pp. 2078
    • Li, H.1
  • 18
    • 55549089660 scopus 로고    scopus 로고
    • Accurate whole human genome sequencing using reversible terminator chemistry
    • Bentley DR et al (2008) Accurate whole human genome sequencing using reversible terminator chemistry. Nature 456:53
    • (2008) Nature , vol.456 , pp. 53
    • Bentley, D.R.1
  • 19
    • 42249087308 scopus 로고    scopus 로고
    • The complete genome of an individual by massively parallel DNA sequencing
    • Wheeler DA et al (2008) The complete genome of an individual by massively parallel DNA sequencing. Nature 452:872
    • (2008) Nature , vol.452 , pp. 872
    • Wheeler, D.A.1
  • 20
    • 0018383167 scopus 로고
    • Rapid nucleotide sequencing of DNA
    • Friedmann T (1979) Rapid nucleotide sequencing of DNA. Am J Hum Genet 31:19
    • (1979) Am J Hum Genet , vol.31 , pp. 19
    • Friedmann, T.1
  • 21
    • 79960597679 scopus 로고    scopus 로고
    • An integrated semiconductor device enabling non-optical genome sequencing
    • Rothberg JM et al (2011) An integrated semiconductor device enabling non-optical genome sequencing. Nature 475:348
    • (2011) Nature , vol.475 , pp. 348
    • Rothberg, J.M.1
  • 22
    • 84860756398 scopus 로고    scopus 로고
    • Performance comparison of benchtop high-throughput sequencing platforms
    • Loman NJ et al (2012) Performance comparison of benchtop high-throughput sequencing platforms. Nat Biotechnol 30 (5):434-439
    • (2012) Nat Biotechnol , vol.30 , Issue.5 , pp. 434-439
    • Loman, N.J.1
  • 23
    • 0036079158 scopus 로고    scopus 로고
    • The human genome browser at UCSC
    • Kent WJ et al (2002) The human genome browser at UCSC. Genome Res 12:996
    • (2002) Genome Res , vol.12 , pp. 996
    • Kent, W.J.1
  • 24
    • 3142727129 scopus 로고    scopus 로고
    • Spectral Repeat Finder (SRF): Identification of repetitive sequences using Fourier transformation
    • Sharma D, Issac B, Raghava GP, Ramaswamy R (2004) Spectral Repeat Finder (SRF): Identification of repetitive sequences using Fourier transformation. Bioinformatics 20:1405
    • (2004) Bioinformatics , vol.20 , pp. 1405
    • Sharma, D.1    Issac, B.2    Raghava, G.P.3    Ramaswamy, R.4
  • 25
    • 34249009076 scopus 로고    scopus 로고
    • Detecting microsatellites within genomes: Significant variation among algorithms
    • Leclercq S, Rivals E, Jarne P (2007) Detecting microsatellites within genomes: Significant variation among algorithms. BMC Bioinformatics 8:125
    • (2007) BMC Bioinformatics , vol.8 , pp. 125
    • Leclercq, S.1    Rivals, E.2    Jarne, P.3
  • 26
    • 84872770867 scopus 로고    scopus 로고
    • Review of tandem repeat search tools: A systematic approach to evaluating algorithmic performance
    • Lim KG, Kwoh CK, Hsu LY, Wirawan A (2013) Review of tandem repeat search tools: A systematic approach to evaluating algorithmic performance. Brief Bioinform 14(1):67-81
    • (2013) Brief Bioinform , vol.14 , Issue.1 , pp. 67-81
    • Lim, K.G.1    Kwoh, C.K.2    Hsu, L.Y.3    Wirawan, A.4
  • 28
    • 0014757386 scopus 로고
    • A general method applicable to the search for similarities in the amino acid sequence of two proteins
    • Needleman SB, Wunsch CD (1970) A general method applicable to the search for similarities in the amino acid sequence of two proteins. J Mol Biol 48:443
    • (1970) J Mol Biol , vol.48 , pp. 443
    • Needleman, S.B.1    Wunsch, C.D.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.