메뉴 건너뛰기




Volumn 9, Issue 3, 2008, Pages

Genome assembly forensics: Finding the elusive mis-assembly

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; AUTOMATION; BACTERIAL GENOME; COMPUTER PROGRAM; EUKARYOTE; GENE REARRANGEMENT; GENE SEQUENCE; GENE STRUCTURE; GENETIC ORGANIZATION; NONHUMAN; NUCLEOTIDE SEQUENCE; VALIDITY; ANIMAL; ARTIFACT; BACILLUS ANTHRACIS; DNA SEQUENCE; DROSOPHILA; GENETICS; GENOME; METHODOLOGY; QUALITY CONTROL; SENSITIVITY AND SPECIFICITY; TANDEM REPEAT;

EID: 45549109750     PISSN: 14747596     EISSN: 1474760X     Source Type: Journal    
DOI: 10.1186/gb-2008-9-3-r55     Document Type: Article
Times cited : (203)

References (46)
  • 5
    • 0037837485 scopus 로고    scopus 로고
    • Genome-wide detection of segmental duplications and potential assembly errors in the human genome sequence
    • 154576 12702206 10.1186/gb-2003-4-4-r25
    • Cheung J Estivill X Khaja R MacDonald JR Lau K Tsui LC Scherer SW Genome-wide detection of segmental duplications and potential assembly errors in the human genome sequence. Genome Biol 2003, 4:R25. 154576 12702206 10.1186/gb-2003-4-4-r25
    • (2003) Genome Biol , vol.4
    • Cheung, J.1    Estivill, X.2    Khaja, R.3    MacDonald, J.R.4    Lau, K.5    Tsui, L.C.6    Scherer, S.W.7
  • 6
    • 16544392954 scopus 로고    scopus 로고
    • Human genome: End of the beginning
    • 10.1038/431915a 15496902
    • Stein LD Human genome: End of the beginning. Nature 2004, 431:915-916. 10.1038/431915a 15496902
    • (2004) Nature , vol.431 , pp. 915-916
    • Stein, L.D.1
  • 7
    • 28944439470 scopus 로고    scopus 로고
    • Beware of mis-assembled genomes
    • 10.1093/bioinformatics/bti769 16332717
    • Salzberg SL Yorke JA Beware of mis-assembled genomes. Bioinformatics 2005, 21:4320-4321. 10.1093/bioinformatics/bti769 16332717
    • (2005) Bioinformatics , vol.21 , pp. 4320-4321
    • Salzberg, S.L.1    Yorke, J.A.2
  • 8
    • 0023988195 scopus 로고
    • Genomic mapping by fingerprinting random clones: A mathematical analysis
    • 10.1016/0888-7543(88)90007-9 3294162
    • Lander ES Waterman MS Genomic mapping by fingerprinting random clones: A mathematical analysis. Genomics 1988, 2:231-239. 10.1016/ 0888-7543(88)90007-9 3294162
    • (1988) Genomics , vol.2 , pp. 231-239
    • Lander, E.S.1    Waterman, M.S.2
  • 9
    • 0028997643 scopus 로고
    • Simple tandem DNA repeats and human genetic disease
    • 42017 7731957 10.1073/pnas.92.9.3636
    • Sutherland GR Richards RI Simple tandem DNA repeats and human genetic disease. Proc Natl Acad Sci USA 1995, 92:3636-3641. 42017 7731957 10.1073/pnas.92.9.3636
    • (1995) Proc Natl Acad Sci USA , vol.92 , pp. 3636-3641
    • Sutherland, G.R.1    Richards, R.I.2
  • 11
    • 0029312158 scopus 로고
    • Toward simplifying and accurately formulating fragment assembly
    • 7497129
    • Myers EW Toward simplifying and accurately formulating fragment assembly. J Comput Biol 1995, 2:275-290. 7497129
    • (1995) J Comput Biol , vol.2 , pp. 275-290
    • Myers, E.W.1
  • 13
    • 0031955116 scopus 로고    scopus 로고
    • Consed: A graphical tool for sequence finishing
    • 9521923
    • Gordon D Abajian C Green P Consed: A graphical tool for sequence finishing. Genome Res 1998, 8:195-202. 9521923
    • (1998) Genome Res , vol.8 , pp. 195-202
    • Gordon, D.1    Abajian, C.2    Green, P.3
  • 15
    • 0036119466 scopus 로고    scopus 로고
    • Computational comparison of human genomic sequence assemblies for a region of chromosome 4
    • 155292 11875030 10.1101/gr.207902. Article published online before print in February 2002
    • Semple CA Morris SW Porteous DJ Evans KL Computational comparison of human genomic sequence assemblies for a region of chromosome 4. Genome Res 2002, 12:424-429. 155292 11875030 10.1101/gr.207902. Article published online before print in February 2002
    • (2002) Genome Res , vol.12 , pp. 424-429
    • Semple, C.A.1    Morris, S.W.2    Porteous, D.J.3    Evans, K.L.4
  • 16
    • 0036995833 scopus 로고    scopus 로고
    • Comparative analysis of human genome assemblies reveals genome-level differences
    • 10.1006/geno.2002.6824 12160725
    • Li S Liao J Cutler G Hoey T Hogenesch JB Cooke MP Schultz PG Ling XB Comparative analysis of human genome assemblies reveals genome-level differences. Genomics 2002, 80:138-139. 10.1006/geno.2002.6824 12160725
    • (2002) Genomics , vol.80 , pp. 138-139
    • Li, S.1    Liao, J.2    Cutler, G.3    Hoey, T.4    Hogenesch, J.B.5    Cooke, M.P.6    Schultz, P.G.7    Ling, X.B.8
  • 17
    • 0035943403 scopus 로고    scopus 로고
    • A comparison of the Celera and Ensembl predicted gene sets reveals little overlap in novel genes
    • 10.1016/S0092-8674(01)00467-6 11534548
    • Hogenesch JB Ching KA Batalov S Su AI Walker JR Zhou Y Kay SA Schultz PG Cooke MP A comparison of the Celera and Ensembl predicted gene sets reveals little overlap in novel genes. Cell 2001, 106:413-415. 10.1016/ S0092-8674(01)00467-6 11534548
    • (2001) Cell , vol.106 , pp. 413-415
    • Hogenesch, J.B.1    Ching, K.A.2    Batalov, S.3    Su, A.I.4    Walker, J.R.5    Zhou, Y.6    Kay, S.A.7    Schultz, P.G.8    Cooke, M.P.9
  • 20
    • 34250210806 scopus 로고    scopus 로고
    • Hawkeye: An interactive visual analytics tool for genome assemblies
    • 1868940 17349036 10.1186/gb-2007-8-3-r34
    • Schatz MC Phillippy AM Shneiderman B Salzberg SL Hawkeye: An interactive visual analytics tool for genome assemblies. Genome Biol 2007, 8:R34. 1868940 17349036 10.1186/gb-2007-8-3-r34
    • (2007) Genome Biol , vol.8
    • Schatz, M.C.1    Phillippy, A.M.2    Shneiderman, B.3    Salzberg, S.L.4
  • 24
    • 21044451909 scopus 로고    scopus 로고
    • A tool for analyzing mate pairs in assemblies (TAMPA)
    • 10.1089/cmb.2005.12.497 15952874
    • Dew IM Walenz B Sutton G A tool for analyzing mate pairs in assemblies (TAMPA). J Comput Biol 2005, 12:497-513. 10.1089/cmb.2005.12.497 15952874
    • (2005) J Comput Biol , vol.12 , pp. 497-513
    • Dew, I.M.1    Walenz, B.2    Sutton, G.3
  • 25
    • 37549051726 scopus 로고    scopus 로고
    • Assembly reconciliation
    • 10.1093/bioinformatics/btm542 18057021
    • Zimin AV Smith DR Sutton G Yorke JA Assembly reconciliation. Bioinformatics 2008, 24:42-45. 10.1093/bioinformatics/btm542 18057021
    • (2008) Bioinformatics , vol.24 , pp. 42-45
    • Zimin, A.V.1    Smith, D.R.2    Sutton, G.3    Yorke, J.A.4
  • 26
    • 33646568477 scopus 로고    scopus 로고
    • DNPTrapper: An assembly editing tool for finishing and analysis of complex repeat regions
    • 1459207 16549006 10.1186/1471-2105-7-155
    • Arner E Tammi MT Tran AN Kindlund E Andersson B DNPTrapper: An assembly editing tool for finishing and analysis of complex repeat regions. BMC Bioinformatics 2006, 7:155. 1459207 16549006 10.1186/1471-2105-7-155
    • (2006) BMC Bioinformatics , vol.7 , pp. 155
    • Arner, E.1    Tammi, M.T.2    Tran, A.N.3    Kindlund, E.4    Andersson, B.5
  • 27
    • 0036204075 scopus 로고    scopus 로고
    • Separation of nearly identical repeats in shotgun assemblies using defined nucleotide positions, DNPs
    • 10.1093/bioinformatics/18.3.379 11934736
    • Tammi MT Arner E Britton T Andersson B Separation of nearly identical repeats in shotgun assemblies using defined nucleotide positions, DNPs. Bioinformatics 2002, 18:379-388. 10.1093/bioinformatics/18.3.379 11934736
    • (2002) Bioinformatics , vol.18 , pp. 379-388
    • Tammi, M.T.1    Arner, E.2    Britton, T.3    Andersson, B.4
  • 29
    • 10644244086 scopus 로고    scopus 로고
    • A time and space efficient algorithm for the substring matching problem
    • Technical Report Universität Hamburg, Zentrum für Bioinformatik
    • Kurtz S A time and space efficient algorithm for the substring matching problem Technical Report Universität Hamburg, Zentrum für Bioinformatik 2003.
    • (2003)
    • Kurtz, S.1
  • 30
    • 0033555906 scopus 로고    scopus 로고
    • Tandem repeats finder: A program to analyze DNA sequences
    • 148217 9862982 10.1093/nar/27.2.573
    • Benson G Tandem repeats finder: A program to analyze DNA sequences. Nucleic Acids Res 1999, 27:573-580. 148217 9862982 10.1093/nar/27.2.573
    • (1999) Nucleic Acids Res , vol.27 , pp. 573-580
    • Benson, G.1
  • 31
    • 0031978181 scopus 로고    scopus 로고
    • Base-calling of automated sequencer traces using phred. II. Error probabilities
    • 9521922
    • Ewing B Green P Base-calling of automated sequencer traces using phred. II. Error probabilities. Genome Res 1998, 8:186-194. 9521922
    • (1998) Genome Res , vol.8 , pp. 186-194
    • Ewing, B.1    Green, P.2
  • 32
    • 0026753344 scopus 로고
    • The accuracy of DNA sequences: Estimating sequence quality
    • 10.1016/S0888-7543(05)80288-5 1358801
    • Churchill GA Waterman MS The accuracy of DNA sequences: Estimating sequence quality. Genomics 1992, 14:89-98. 10.1016/S0888-7543(05)80288-5 1358801
    • (1992) Genomics , vol.14 , pp. 89-98
    • Churchill, G.A.1    Waterman, M.S.2
  • 34
    • 0036606576 scopus 로고    scopus 로고
    • Fast algorithms for large-scale genome alignment and comparison
    • 117189 12034836 10.1093/nar/30.11.2478
    • Delcher AL Phillippy A Carlton J Salzberg SL Fast algorithms for large-scale genome alignment and comparison. Nucleic Acids Res 2002, 30:2478-2483. 117189 12034836 10.1093/nar/30.11.2478
    • (2002) Nucleic Acids Res , vol.30 , pp. 2478-2483
    • Delcher, A.L.1    Phillippy, A.2    Carlton, J.3    Salzberg, S.L.4
  • 37
    • 19344372045 scopus 로고    scopus 로고
    • The genome Assembly Archive: A new public resource
    • 516794 15367931 10.1371/journal.pbio.0020285
    • Salzberg SL Church D DiCuccio M Yaschenko E Ostell J The genome Assembly Archive: A new public resource. PLoS Biol 2004, 2:E285. 516794 15367931 10.1371/journal.pbio.0020285
    • (2004) PLoS Biol , vol.2
    • Salzberg, S.L.1    Church, D.2    DiCuccio, M.3    Yaschenko, E.4    Ostell, J.5
  • 40
    • 0141853948 scopus 로고    scopus 로고
    • PCAP: A whole-genome assembly program
    • 403719 12952883 10.1101/gr.1390403
    • Huang X Wang J Aluru S Yang SP Hillier L PCAP: A whole-genome assembly program. Genome Res 2003, 13:2164-2170. 403719 12952883 10.1101/ gr.1390403
    • (2003) Genome Res , vol.13 , pp. 2164-2170
    • Huang, X.1    Wang, J.2    Aluru, S.3    Yang, S.P.4    Hillier, L.5
  • 42
    • 0037263854 scopus 로고    scopus 로고
    • The phusion assembler
    • 430959 12529309 10.1101/gr.731003
    • Mullikin JC Ning Z The phusion assembler. Genome Res 2003, 13:81-90. 430959 12529309 10.1101/gr.731003
    • (2003) Genome Res , vol.13 , pp. 81-90
    • Mullikin, J.C.1    Ning, Z.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.