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Volumn 60, Issue C, 2004, Pages 193-248

Shotgun Sequence Assembly

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EID: 34547312505     PISSN: 00652458     EISSN: None     Source Type: Book Series    
DOI: 10.1016/S0065-2458(03)60006-9     Document Type: Review
Times cited : (26)

References (137)
  • 1
    • 0020465927 scopus 로고
    • Nucleotide sequence of bacteriophage lambda DNA
    • Sanger F., et al. Nucleotide sequence of bacteriophage lambda DNA. J. Mol. Biol. 162 4 (1982) 729-773
    • (1982) J. Mol. Biol. , vol.162 , Issue.4 , pp. 729-773
    • Sanger, F.1
  • 2
    • 0020480482 scopus 로고
    • Automation of the computer handling of gel reading data produced by the shotgun method of DNA sequencing
    • Staden R. Automation of the computer handling of gel reading data produced by the shotgun method of DNA sequencing. Nucleic Acids Res. 10 (1982) 4731-4751
    • (1982) Nucleic Acids Res. , vol.10 , pp. 4731-4751
    • Staden, R.1
  • 3
    • 0018680552 scopus 로고
    • Computer programs for the assembly of DNA sequences
    • Gingeras T.R., et al. Computer programs for the assembly of DNA sequences. Nucleic Acids Res. 7 2 (1979) 529-545
    • (1979) Nucleic Acids Res. , vol.7 , Issue.2 , pp. 529-545
    • Gingeras, T.R.1
  • 4
    • 0029653518 scopus 로고
    • Whole-genome random sequencing and assembly of Haemophilus influenzae Rd
    • Fleischmann R.D., et al. Whole-genome random sequencing and assembly of Haemophilus influenzae Rd. Science 269 5223 (1995) 496-512
    • (1995) Science , vol.269 , Issue.5223 , pp. 496-512
    • Fleischmann, R.D.1
  • 5
    • 0001899550 scopus 로고
    • TIGR assembler: A new tool for assembling large shotgun sequencing projects
    • Sutton G.G., et al. TIGR assembler: A new tool for assembling large shotgun sequencing projects. Genome Science and Technology 1 (1995) 9-19
    • (1995) Genome Science and Technology , vol.1 , pp. 9-19
    • Sutton, G.G.1
  • 6
    • 0030972827 scopus 로고    scopus 로고
    • Against a whole-genome shotgun
    • Green P. Against a whole-genome shotgun. Genome Res. 7 5 (1997) 410-417
    • (1997) Genome Res. , vol.7 , Issue.5 , pp. 410-417
    • Green, P.1
  • 7
    • 0034708480 scopus 로고    scopus 로고
    • The genome sequence of Drosophila melanogaster
    • Adams M.D., et al. The genome sequence of Drosophila melanogaster. Science 287 5461 (2000) 2185-2195
    • (2000) Science , vol.287 , Issue.5461 , pp. 2185-2195
    • Adams, M.D.1
  • 8
    • 0034708758 scopus 로고    scopus 로고
    • A whole-genome assembly of Drosophila
    • Myers E.W., et al. A whole-genome assembly of Drosophila. Science 287 5461 (2000) 2196-2204
    • (2000) Science , vol.287 , Issue.5461 , pp. 2196-2204
    • Myers, E.W.1
  • 9
    • 0035895505 scopus 로고    scopus 로고
    • The sequence of the human genome
    • Venter J.C., et al. The sequence of the human genome. Science 291 5507 (2001) 1304-1351
    • (2001) Science , vol.291 , Issue.5507 , pp. 1304-1351
    • Venter, J.C.1
  • 10
    • 2042437650 scopus 로고    scopus 로고
    • Initial sequencing and analysis of the human genome
    • Consortium I.H.G.S. Initial sequencing and analysis of the human genome. Nature 409 (2001) 860-921
    • (2001) Nature , vol.409 , pp. 860-921
    • Consortium, I.H.G.S.1
  • 11
    • 0036119466 scopus 로고    scopus 로고
    • Computational comparison of human genomic sequence assemblies for a region of chromosome 4
    • Semple C.A., et al. Computational comparison of human genomic sequence assemblies for a region of chromosome 4. Genome Res. 12 3 (2002) 424-429
    • (2002) Genome Res. , vol.12 , Issue.3 , pp. 424-429
    • Semple, C.A.1
  • 12
    • 0035865091 scopus 로고    scopus 로고
    • Computational comparison of two draft sequences of the human genome
    • Aach J., et al. Computational comparison of two draft sequences of the human genome. Nature 409 6822 (2001) 856-859
    • (2001) Nature , vol.409 , Issue.6822 , pp. 856-859
    • Aach, J.1
  • 13
    • 0037453070 scopus 로고    scopus 로고
    • The independence of our genome assemblies
    • Adams M.D., et al. The independence of our genome assemblies. Proc. Natl. Acad. Sci. USA 100 6 (2003) 3025-3026
    • (2003) Proc. Natl. Acad. Sci. USA , vol.100 , Issue.6 , pp. 3025-3026
    • Adams, M.D.1
  • 14
    • 0037453096 scopus 로고    scopus 로고
    • More on the sequencing of the human genome
    • author reply 3025-3026
    • Waterston R.H., Lander E.S., and Sulston J.E. More on the sequencing of the human genome. Proc. Natl. Acad. Sci. USA 100 6 (2003) 3022-3024 author reply 3025-3026
    • (2003) Proc. Natl. Acad. Sci. USA , vol.100 , Issue.6 , pp. 3022-3024
    • Waterston, R.H.1    Lander, E.S.2    Sulston, J.E.3
  • 16
    • 0037007013 scopus 로고    scopus 로고
    • Whole-genome disassembly
    • Green P. Whole-genome disassembly. Proc. Natl. Acad. Sci. USA 99 7 (2002) 4143-4144
    • (2002) Proc. Natl. Acad. Sci. USA , vol.99 , Issue.7 , pp. 4143-4144
    • Green, P.1
  • 17
    • 0037007087 scopus 로고    scopus 로고
    • On the sequencing and assembly of the human genome
    • Myers E.W., et al. On the sequencing and assembly of the human genome. Proc. Natl. Acad. Sci. USA 99 7 (2002) 4145-4146
    • (2002) Proc. Natl. Acad. Sci. USA , vol.99 , Issue.7 , pp. 4145-4146
    • Myers, E.W.1
  • 18
    • 0036144823 scopus 로고    scopus 로고
    • ARACHNE: a whole-genome shotgun assembler
    • Batzoglou S., et al. ARACHNE: a whole-genome shotgun assembler. Genome Res. 12 1 (2002) 177-189
    • (2002) Genome Res. , vol.12 , Issue.1 , pp. 177-189
    • Batzoglou, S.1
  • 19
    • 0037267048 scopus 로고    scopus 로고
    • Whole-genome sequence assembly for Mammalian genomes: arachne 2
    • Jaffe D.B., et al. Whole-genome sequence assembly for Mammalian genomes: arachne 2. Genome Res. 13 1 (2003) 91-96
    • (2003) Genome Res. , vol.13 , Issue.1 , pp. 91-96
    • Jaffe, D.B.1
  • 20
    • 0037263854 scopus 로고    scopus 로고
    • The phusion assembler
    • Mullikin J.C., and Ning Z. The phusion assembler. Genome Res. 13 1 (2003) 81-90
    • (2003) Genome Res. , vol.13 , Issue.1 , pp. 81-90
    • Mullikin, J.C.1    Ning, Z.2
  • 22
    • 0037162885 scopus 로고    scopus 로고
    • Whole-genome shotgun assembly and analysis of the genome of Fugu rubripes
    • Aparicio S., et al. Whole-genome shotgun assembly and analysis of the genome of Fugu rubripes. Science 297 5585 (2002) 1301-1310
    • (2002) Science , vol.297 , Issue.5585 , pp. 1301-1310
    • Aparicio, S.1
  • 23
    • 1542563409 scopus 로고    scopus 로고
    • Initial sequencing and comparative analysis of the mouse genome
    • Waterston R.H., et al. Initial sequencing and comparative analysis of the mouse genome. Nature 420 6915 (2002) 520-562
    • (2002) Nature , vol.420 , Issue.6915 , pp. 520-562
    • Waterston, R.H.1
  • 25
    • 0141596080 scopus 로고    scopus 로고
    • The dog genome: survey sequencing and comparative analysis
    • Kirkness E.F., et al. The dog genome: survey sequencing and comparative analysis. Science 301 5641 (2003) 1898-1903
    • (2003) Science , vol.301 , Issue.5641 , pp. 1898-1903
    • Kirkness, E.F.1
  • 26
    • 2242464840 scopus 로고    scopus 로고
    • The draft genome of Ciona intestinalis: insights into chordate and vertebrate origins
    • Dehal P., et al. The draft genome of Ciona intestinalis: insights into chordate and vertebrate origins. Science 298 5601 (2002) 2157-2167
    • (2002) Science , vol.298 , Issue.5601 , pp. 2157-2167
    • Dehal, P.1
  • 27
    • 0035432364 scopus 로고    scopus 로고
    • Strategies for the systematic sequencing of complex genomes
    • Green E.D. Strategies for the systematic sequencing of complex genomes. Nat. Rev. Genet. 2 8 (2001) 573-583
    • (2001) Nat. Rev. Genet. , vol.2 , Issue.8 , pp. 573-583
    • Green, E.D.1
  • 28
    • 0034760329 scopus 로고    scopus 로고
    • A clone-array pooled shotgun strategy for sequencing large genomes
    • Cai W.W., et al. A clone-array pooled shotgun strategy for sequencing large genomes. Genome Res. 11 10 (2001) 1619-1623
    • (2001) Genome Res. , vol.11 , Issue.10 , pp. 1619-1623
    • Cai, W.W.1
  • 29
    • 0023988195 scopus 로고
    • Genomic mapping by fingerprinting random clones: A mathematical analysis
    • Lander E.S., and Waterman M.S. Genomic mapping by fingerprinting random clones: A mathematical analysis. Genomics 2 3 (1988) 231-239
    • (1988) Genomics , vol.2 , Issue.3 , pp. 231-239
    • Lander, E.S.1    Waterman, M.S.2
  • 31
    • 0033452647 scopus 로고    scopus 로고
    • Sequencing a genome by walking with clone-end sequences: A mathematical analysis
    • Batzoglou S., et al. Sequencing a genome by walking with clone-end sequences: A mathematical analysis. Genome Res. 9 (1999) 1163-1174
    • (1999) Genome Res. , vol.9 , pp. 1163-1174
    • Batzoglou, S.1
  • 32
    • 0041523918 scopus 로고    scopus 로고
    • Estimating the repeat structure and length of DNA sequences using ell-tuples
    • Li X., and Waterman M.S. Estimating the repeat structure and length of DNA sequences using ell-tuples. Genome Res. 13 8 (2003) 1916-1922
    • (2003) Genome Res. , vol.13 , Issue.8 , pp. 1916-1922
    • Li, X.1    Waterman, M.S.2
  • 33
    • 0026328675 scopus 로고
    • Genomic mapping by anchoring random clones: A mathematical analysis
    • Arratia R., et al. Genomic mapping by anchoring random clones: A mathematical analysis. Genomics 11 4 (1991) 806-827
    • (1991) Genomics , vol.11 , Issue.4 , pp. 806-827
    • Arratia, R.1
  • 34
    • 0028987725 scopus 로고
    • Pairwise end sequencing: A unified approach to genomic mapping and sequencing
    • Roach J.C., et al. Pairwise end sequencing: A unified approach to genomic mapping and sequencing. Genomics 26 (1995) 345-353
    • (1995) Genomics , vol.26 , pp. 345-353
    • Roach, J.C.1
  • 35
    • 0028914393 scopus 로고
    • Genomic mapping by end-characterized random clones: A mathematical analysis
    • Port E., et al. Genomic mapping by end-characterized random clones: A mathematical analysis. Genomics 26 1 (1995) 84-100
    • (1995) Genomics , vol.26 , Issue.1 , pp. 84-100
    • Port, E.1
  • 37
    • 0030859961 scopus 로고    scopus 로고
    • Representation of cloned genomic sequences in two sequencing vectors: correlation of DNA sequence and subclone distribution
    • Chissoe S.L., et al. Representation of cloned genomic sequences in two sequencing vectors: correlation of DNA sequence and subclone distribution. Nucleic Acids Res. 25 15 (1997) 2960-2966
    • (1997) Nucleic Acids Res. , vol.25 , Issue.15 , pp. 2960-2966
    • Chissoe, S.L.1
  • 38
    • 0022965004 scopus 로고
    • Specific enzymatic amplification of DNA in vitro: the polymerase chain reaction
    • Mullis K., et al. Specific enzymatic amplification of DNA in vitro: the polymerase chain reaction. Cold Spring Harb. Symp. Quant. Biol. 51 Pt 1 (1986) 263-273
    • (1986) Cold Spring Harb. Symp. Quant. Biol. , vol.51 PART 1 , pp. 263-273
    • Mullis, K.1
  • 39
    • 0026862833 scopus 로고
    • Multiplex polymerase chain reaction
    • Burgart L.J., et al. Multiplex polymerase chain reaction. Mod. Pathol. 5 3 (1992) 320-323
    • (1992) Mod. Pathol. , vol.5 , Issue.3 , pp. 320-323
    • Burgart, L.J.1
  • 40
    • 0033572258 scopus 로고    scopus 로고
    • Optimized multiplex PCR: efficiently closing a whole-genome shotgun sequencing project
    • Tettelin H., et al. Optimized multiplex PCR: efficiently closing a whole-genome shotgun sequencing project. Genomics 62 3 (1999) 500-507
    • (1999) Genomics , vol.62 , Issue.3 , pp. 500-507
    • Tettelin, H.1
  • 44
    • 0035054380 scopus 로고    scopus 로고
    • Automated finishing with autofinish
    • Gordon D., Desmarais C., and Green P. Automated finishing with autofinish. Genome Res. 11 4 (2001) 614-625
    • (2001) Genome Res. , vol.11 , Issue.4 , pp. 614-625
    • Gordon, D.1    Desmarais, C.2    Green, P.3
  • 45
    • 0031955116 scopus 로고    scopus 로고
    • Consed: A graphical tool for sequence finishing
    • Gordon D., Abajian C., and Green P. Consed: A graphical tool for sequence finishing. Genome Res. 8 (1998) 195-202
    • (1998) Genome Res. , vol.8 , pp. 195-202
    • Gordon, D.1    Abajian, C.2    Green, P.3
  • 46
    • 0036372889 scopus 로고    scopus 로고
    • EULER-PCR: finishing experiments for repeat resolution
    • Mulyukov Z., and Pevzner P.A. EULER-PCR: finishing experiments for repeat resolution. Pac. Symp. Biocomput. (2002) 199-210
    • (2002) Pac. Symp. Biocomput. , pp. 199-210
    • Mulyukov, Z.1    Pevzner, P.A.2
  • 47
    • 0033858199 scopus 로고    scopus 로고
    • Microsatellites in different eukaryotic genomes: survey and analysis
    • Toth G., Gaspari Z., and Jurka J. Microsatellites in different eukaryotic genomes: survey and analysis. Genome Res. 10 7 (2000) 967-981
    • (2000) Genome Res. , vol.10 , Issue.7 , pp. 967-981
    • Toth, G.1    Gaspari, Z.2    Jurka, J.3
  • 48
    • 0029312158 scopus 로고
    • Toward simplifying and accurately formulating fragment assembly
    • Myers E.W. Toward simplifying and accurately formulating fragment assembly. J. Comp. Bio. 2 2 (1995) 275-290
    • (1995) J. Comp. Bio. , vol.2 , Issue.2 , pp. 275-290
    • Myers, E.W.1
  • 52
    • 84976693225 scopus 로고
    • Algorithms for some string matching problems arising in molecular genetics
    • Peltola H., et al. Algorithms for some string matching problems arising in molecular genetics. Proc. Information Processing (1983)
    • (1983) Proc. Information Processing
    • Peltola, H.1
  • 53
    • 0347941370 scopus 로고    scopus 로고
    • Approximating shortest superstrings
    • Teng S., and Yao F.F. Approximating shortest superstrings. SIAM J. Computing 26 2 (1997) 410-417
    • (1997) SIAM J. Computing , vol.26 , Issue.2 , pp. 410-417
    • Teng, S.1    Yao, F.F.2
  • 54
    • 0342784101 scopus 로고    scopus 로고
    • A 2 2/3-approximation algorithm for the shortest superstring problem
    • Armen C., and Stein C. A 2 2/3-approximation algorithm for the shortest superstring problem. Proc. Combinatorial Pattern Matching (1996)
    • (1996) Proc. Combinatorial Pattern Matching
    • Armen, C.1    Stein, C.2
  • 56
    • 0019887799 scopus 로고
    • Identification of common molecular subsequences
    • Smith T.F., and Waterman M.S. Identification of common molecular subsequences. J. Mol. Biol. 147 1 (1981) 195-197
    • (1981) J. Mol. Biol. , vol.147 , Issue.1 , pp. 195-197
    • Smith, T.F.1    Waterman, M.S.2
  • 57
    • 0021760072 scopus 로고
    • SEQAID: a DNA sequence assembling program based on a mathematical model
    • Peltola H., Soderlund H., and Ukkonen E. SEQAID: a DNA sequence assembling program based on a mathematical model. Nucleic Acids Res. 12 1 (1984) 307-321
    • (1984) Nucleic Acids Res. , vol.12 , Issue.1 , pp. 307-321
    • Peltola, H.1    Soderlund, H.2    Ukkonen, E.3
  • 58
    • 0029197192 scopus 로고
    • Combinatorial algorithms for DNA sequence assembly
    • Kececioglu J.D., and Myers E.W. Combinatorial algorithms for DNA sequence assembly. Algorithmica 13 (1995) 7-51
    • (1995) Algorithmica , vol.13 , pp. 7-51
    • Kececioglu, J.D.1    Myers, E.W.2
  • 59
    • 0029312687 scopus 로고
    • A new algorithm for DNA sequence assembly
    • Idury R.M., and Waterman M.S. A new algorithm for DNA sequence assembly. J. Comp. Bio. 2 2 (1995) 291-306
    • (1995) J. Comp. Bio. , vol.2 , Issue.2 , pp. 291-306
    • Idury, R.M.1    Waterman, M.S.2
  • 60
    • 0035859921 scopus 로고    scopus 로고
    • An Eulerian path approach to DNA fragment assembly
    • Pevzner P.A., Tang H., and Waterman M.S. An Eulerian path approach to DNA fragment assembly. Proc. Natl. Acad. Sci. USA 98 17 (2001) 9748-9753
    • (2001) Proc. Natl. Acad. Sci. USA , vol.98 , Issue.17 , pp. 9748-9753
    • Pevzner, P.A.1    Tang, H.2    Waterman, M.S.3
  • 61
    • 0035232164 scopus 로고    scopus 로고
    • Fragment assembly with double-barreled data
    • Pevzner P.A., and Tang H. Fragment assembly with double-barreled data. Bioinformatics 17 Suppl 1 (2001) S225-S233
    • (2001) Bioinformatics , vol.17 , Issue.SUPPL. 1
    • Pevzner, P.A.1    Tang, H.2
  • 63
    • 0036644865 scopus 로고    scopus 로고
    • Genome sequence assembly: algorithms and issues
    • Pop M., Salzberg S.L., and Shumway M. Genome sequence assembly: algorithms and issues. IEEE Computer 35 7 (2002) 47-54
    • (2002) IEEE Computer , vol.35 , Issue.7 , pp. 47-54
    • Pop, M.1    Salzberg, S.L.2    Shumway, M.3
  • 64
    • 0032849859 scopus 로고    scopus 로고
    • CAP3: A DNA sequence assembly program
    • Huang X., and Madan A. CAP3: A DNA sequence assembly program. Genome Res. 9 (1999) 868-877
    • (1999) Genome Res. , vol.9 , pp. 868-877
    • Huang, X.1    Madan, A.2
  • 65
    • 0035116038 scopus 로고    scopus 로고
    • Sequence and analysis of the Arabidopsis genome
    • Bevan M., et al. Sequence and analysis of the Arabidopsis genome. Curr. Opin. Plant. Biol. 4 2 (2001) 105-110
    • (2001) Curr. Opin. Plant. Biol. , vol.4 , Issue.2 , pp. 105-110
    • Bevan, M.1
  • 66
    • 0034837599 scopus 로고    scopus 로고
    • Assembly of the working draft of the human genome with GigAssembler
    • Kent W.J., and Haussler D. Assembly of the working draft of the human genome with GigAssembler. Genome Res. 11 9 (2001) 1541-1548
    • (2001) Genome Res. , vol.11 , Issue.9 , pp. 1541-1548
    • Kent, W.J.1    Haussler, D.2
  • 67
    • 0024980741 scopus 로고
    • A common language for physical mapping of the human genome
    • Olson M., et al. A common language for physical mapping of the human genome. Science 245 4925 (1989) 1434-1435
    • (1989) Science , vol.245 , Issue.4925 , pp. 1434-1435
    • Olson, M.1
  • 68
    • 18444378733 scopus 로고    scopus 로고
    • RePS: a sequence assembler that masks exact repeats identified from the shotgun data
    • Wang J., et al. RePS: a sequence assembler that masks exact repeats identified from the shotgun data. Genome Res. 12 5 (2002) 824-831
    • (2002) Genome Res. , vol.12 , Issue.5 , pp. 824-831
    • Wang, J.1
  • 69
    • 0035224746 scopus 로고    scopus 로고
    • Design of a compartmentalized shotgun assembler for the human genome
    • Huson D.H., et al. Design of a compartmentalized shotgun assembler for the human genome. Bioinformatics 17 Suppl 1 (2001) S132-S139
    • (2001) Bioinformatics , vol.17 , Issue.SUPPL. 1
    • Huson, D.H.1
  • 71
    • 0029387798 scopus 로고
    • Genetic algorithms, operators, and DNA fragment assembly
    • Parsons R.J., Forrest S., and Burks C. Genetic algorithms, operators, and DNA fragment assembly. Machine Learning 21 (1995) 11-33
    • (1995) Machine Learning , vol.21 , pp. 11-33
    • Parsons, R.J.1    Forrest, S.2    Burks, C.3
  • 74
    • 0012748276 scopus 로고    scopus 로고
    • DNA sequencing and string learning
    • Jiang T., and Li M. DNA sequencing and string learning. Math. Sys. Theory 29 (1996) 387-405
    • (1996) Math. Sys. Theory , vol.29 , pp. 387-405
    • Jiang, T.1    Li, M.2
  • 75
    • 0030784674 scopus 로고    scopus 로고
    • Satellite DNA repeat sequence variation is low in three species of burying beetles in the genus Nicrophorus (Coleoptera: Silphidae)
    • King L.M., and Cummings M.P. Satellite DNA repeat sequence variation is low in three species of burying beetles in the genus Nicrophorus (Coleoptera: Silphidae). Mol. Biol. Evol. 14 11 (1997) 1088-1095
    • (1997) Mol. Biol. Evol. , vol.14 , Issue.11 , pp. 1088-1095
    • King, L.M.1    Cummings, M.P.2
  • 79
    • 0033832184 scopus 로고    scopus 로고
    • A case study in genome-level fragment assembly
    • Chen T., and Skiena S.S. A case study in genome-level fragment assembly. Bioinformatics 16 (2000) 494-500
    • (2000) Bioinformatics , vol.16 , pp. 494-500
    • Chen, T.1    Skiena, S.S.2
  • 81
    • 0027681165 scopus 로고
    • Suffix arrays: A new method for on-line string searches
    • Manber U., and Myers E.W. Suffix arrays: A new method for on-line string searches. SIAM J. Computing 22 (1993) 935-948
    • (1993) SIAM J. Computing , vol.22 , pp. 935-948
    • Manber, U.1    Myers, E.W.2
  • 82
    • 0001704377 scopus 로고
    • On-line construction of suffix-trees
    • Ukkonen E. On-line construction of suffix-trees. Algorithmica 14 (1995) 249-260
    • (1995) Algorithmica , vol.14 , pp. 249-260
    • Ukkonen, E.1
  • 83
    • 0016942292 scopus 로고
    • A space-economical suffix tree construction algorithm
    • McCreight E.M. A space-economical suffix tree construction algorithm. J. ACM 23 (1976) 262-272
    • (1976) J. ACM , vol.23 , pp. 262-272
    • McCreight, E.M.1
  • 84
    • 0014757386 scopus 로고
    • A general method applicable to the search for similarities in the amino acid sequence of two proteins
    • Needleman S.B., and Wunsch C.D. A general method applicable to the search for similarities in the amino acid sequence of two proteins. J. Mol. Biol. 48 (1970) 443-453
    • (1970) J. Mol. Biol. , vol.48 , pp. 443-453
    • Needleman, S.B.1    Wunsch, C.D.2
  • 85
    • 0023984847 scopus 로고
    • Optimal alignments in linear space
    • Myers E.W., and Miller W. Optimal alignments in linear space. CABIOS 4 (1988) 11-17
    • (1988) CABIOS , vol.4 , pp. 11-17
    • Myers, E.W.1    Miller, W.2
  • 86
    • 0023012946 scopus 로고
    • An O(nd) difference algorithm and its variations
    • Myers E.W. An O(nd) difference algorithm and its variations. Algorithmica 1 (1986) 251-266
    • (1986) Algorithmica , vol.1 , pp. 251-266
    • Myers, E.W.1
  • 88
    • 0025183708 scopus 로고
    • Basic local alignment search tool
    • Altschul S.F., et al. Basic local alignment search tool. J. Mol. Biol. 215 (1990) 403-410
    • (1990) J. Mol. Biol. , vol.215 , pp. 403-410
    • Altschul, S.F.1
  • 89
    • 0023989064 scopus 로고
    • Improved tools for biological sequence comparison
    • Pearson W.R., and Lipman D.J. Improved tools for biological sequence comparison. Proc. Natl. Acad. Sci. USA 85 (1988) 2444-2448
    • (1988) Proc. Natl. Acad. Sci. USA , vol.85 , pp. 2444-2448
    • Pearson, W.R.1    Lipman, D.J.2
  • 90
    • 0032990711 scopus 로고    scopus 로고
    • AMASS: A structured pattern matching approach to shotgun sequence assembly
    • Kim S., and Segre A.M. AMASS: A structured pattern matching approach to shotgun sequence assembly. J. Comp. Bio. 6 2 (1999) 163-186
    • (1999) J. Comp. Bio. , vol.6 , Issue.2 , pp. 163-186
    • Kim, S.1    Segre, A.M.2
  • 92
    • 0029933276 scopus 로고    scopus 로고
    • An improved sequence assembly program
    • Huang X. An improved sequence assembly program. Genomics 33 (1996) 21-31
    • (1996) Genomics , vol.33 , pp. 21-31
    • Huang, X.1
  • 93
    • 0042161822 scopus 로고    scopus 로고
    • Correcting errors in shotgun sequences
    • Tammi M.T., et al. Correcting errors in shotgun sequences. Nucleic Acids Res. 31 15 (2003) 4663-4672
    • (2003) Nucleic Acids Res. , vol.31 , Issue.15 , pp. 4663-4672
    • Tammi, M.T.1
  • 95
    • 0141853948 scopus 로고    scopus 로고
    • PCAP: A whole-genome assembly program
    • Huang X., et al. PCAP: A whole-genome assembly program. Genome Res. 13 9 (2003) 2164-2170
    • (2003) Genome Res. , vol.13 , Issue.9 , pp. 2164-2170
    • Huang, X.1
  • 96
    • 0031978181 scopus 로고    scopus 로고
    • Base-calling of automated sequencer traces using phred. II. Error probabilities
    • Ewing B., and Green P. Base-calling of automated sequencer traces using phred. II. Error probabilities. Genome Res. 8 3 (1998) 186-194
    • (1998) Genome Res. , vol.8 , Issue.3 , pp. 186-194
    • Ewing, B.1    Green, P.2
  • 97
    • 0031955518 scopus 로고    scopus 로고
    • Base-calling of automated sequencer traces using phred. I. Accuracy assessment
    • Ewing B., et al. Base-calling of automated sequencer traces using phred. I. Accuracy assessment. Genome Res. 8 3 (1998) 175-185
    • (1998) Genome Res. , vol.8 , Issue.3 , pp. 175-185
    • Ewing, B.1
  • 98
    • 0036137277 scopus 로고    scopus 로고
    • DNA sequence quality trimming and vector removal
    • Chou H.H., and Holmes M.H. DNA sequence quality trimming and vector removal. Bioinformatics 17 12 (2001) 1093-1104
    • (2001) Bioinformatics , vol.17 , Issue.12 , pp. 1093-1104
    • Chou, H.H.1    Holmes, M.H.2
  • 100
    • 0035756173 scopus 로고    scopus 로고
    • Optimally separating sequences
    • Myers E.W. Optimally separating sequences. Genome Informatics 12 (2001) 165-174
    • (2001) Genome Informatics , vol.12 , pp. 165-174
    • Myers, E.W.1
  • 101
    • 0036204075 scopus 로고    scopus 로고
    • Separation of nearly identical repeats in shotgun assemblies using defined nucleotide positions, DNPs
    • Tammi M.T., et al. Separation of nearly identical repeats in shotgun assemblies using defined nucleotide positions, DNPs. Bioinformatics 18 3 (2002) 379-388
    • (2002) Bioinformatics , vol.18 , Issue.3 , pp. 379-388
    • Tammi, M.T.1
  • 102
    • 0037212880 scopus 로고    scopus 로고
    • TRAP: Tandem Repeat Assembly Program produces improved shotgun assemblies of repetitive sequences
    • Tammi M.T., Arner E., and Andersson B. TRAP: Tandem Repeat Assembly Program produces improved shotgun assemblies of repetitive sequences. Comput. Methods Programs Biomed. 70 1 (2003) 47-59
    • (2003) Comput. Methods Programs Biomed. , vol.70 , Issue.1 , pp. 47-59
    • Tammi, M.T.1    Arner, E.2    Andersson, B.3
  • 104
    • 0034831138 scopus 로고    scopus 로고
    • Segmental duplications: organization and impact within the current human genome project assembly
    • Bailey J.A., et al. Segmental duplications: organization and impact within the current human genome project assembly. Genome Res. 11 (2001) 1005-1017
    • (2001) Genome Res. , vol.11 , pp. 1005-1017
    • Bailey, J.A.1
  • 105
    • 77956757764 scopus 로고    scopus 로고
    • Fragment assembly with double barreled data
    • Pevzner P., and Tang H. Fragment assembly with double barreled data. ISMB'01 (2001)
    • (2001) ISMB'01
    • Pevzner, P.1    Tang, H.2
  • 107
    • 0030672551 scopus 로고    scopus 로고
    • ReAligner: A program for refining DNA sequence multi-alignments
    • Anson E.L., and Myers E.W. ReAligner: A program for refining DNA sequence multi-alignments. RECOMB'97 (1997)
    • (1997) RECOMB'97
    • Anson, E.L.1    Myers, E.W.2
  • 108
    • 0026753344 scopus 로고
    • The accuracy of DNA sequences: estimating sequence quality
    • Churchill G.A., and Waterman M.S. The accuracy of DNA sequences: estimating sequence quality. Genomics 14 1 (1992) 89-98
    • (1992) Genomics , vol.14 , Issue.1 , pp. 89-98
    • Churchill, G.A.1    Waterman, M.S.2
  • 109
    • 0029068220 scopus 로고
    • The application of numerical estimates of base calling accuracy to DNA sequencing projects
    • Bonfield J.K., and Staden R. The application of numerical estimates of base calling accuracy to DNA sequencing projects. Nucleic Acids Res. 23 8 (1995) 1406-1410
    • (1995) Nucleic Acids Res. , vol.23 , Issue.8 , pp. 1406-1410
    • Bonfield, J.K.1    Staden, R.2
  • 110
    • 0141519284 scopus 로고    scopus 로고
    • Whole-genome shotgun optical mapping of rhodobacter sphaeroides strain 2.4.1 and its use for whole-genome shotgun sequence assembly
    • Zhou S., et al. Whole-genome shotgun optical mapping of rhodobacter sphaeroides strain 2.4.1 and its use for whole-genome shotgun sequence assembly. Genome Res. 13 9 (2003) 2142-2151
    • (2003) Genome Res. , vol.13 , Issue.9 , pp. 2142-2151
    • Zhou, S.1
  • 112
    • 0033005036 scopus 로고    scopus 로고
    • Error checking and graphical representation of multiple-complete-digest (MCD) restriction-fragment maps
    • Thayer E.C., Olson M.V., and Karp R.M. Error checking and graphical representation of multiple-complete-digest (MCD) restriction-fragment maps. Genome Res. 9 1 (1999) 79-90
    • (1999) Genome Res. , vol.9 , Issue.1 , pp. 79-90
    • Thayer, E.C.1    Olson, M.V.2    Karp, R.M.3
  • 113
    • 0346505466 scopus 로고    scopus 로고
    • Hierarchical scaffolding with bambus
    • Pop M., Kosack D., and Salzberg S.L. Hierarchical scaffolding with bambus. Genome Res. 14 1 (2004) 149-159
    • (2004) Genome Res. , vol.14 , Issue.1 , pp. 149-159
    • Pop, M.1    Kosack, D.2    Salzberg, S.L.3
  • 115
    • 0027413767 scopus 로고
    • An experimentally derived data set constructed for testing large-scale DNA sequence assembly algorithms
    • Seto D., Koop B.F., and Hood L. An experimentally derived data set constructed for testing large-scale DNA sequence assembly algorithms. Genomics 15 (1993) 673-676
    • (1993) Genomics , vol.15 , pp. 673-676
    • Seto, D.1    Koop, B.F.2    Hood, L.3
  • 116
    • 0028679357 scopus 로고
    • A quantitative comparison of DNA sequence assembly programs
    • Miller M.J., and Powell J.I. A quantitative comparison of DNA sequence assembly programs. J. Comp. Bio. 1 (1994) 257-269
    • (1994) J. Comp. Bio. , vol.1 , pp. 257-269
    • Miller, M.J.1    Powell, J.I.2
  • 117
    • 45449099820 scopus 로고    scopus 로고
    • Comparing assemblies using fragments and mate-pairs
    • Springer-Verlag
    • Huson D.H., et al. Comparing assemblies using fragments and mate-pairs. Workshop on Algorithms in Bioinformatics (2001), Springer-Verlag
    • (2001) Workshop on Algorithms in Bioinformatics
    • Huson, D.H.1
  • 118
    • 0027252551 scopus 로고
    • Artificially generated data sets for testing DNA sequence assembly algorithms
    • Engle M.L., and Burks C. Artificially generated data sets for testing DNA sequence assembly algorithms. Genomics 16 (1993) 286-288
    • (1993) Genomics , vol.16 , pp. 286-288
    • Engle, M.L.1    Burks, C.2
  • 119
    • 0033291476 scopus 로고    scopus 로고
    • A dataset generator for whole genome shotgun sequencing
    • Myers G. A dataset generator for whole genome shotgun sequencing. Proc. Int. Conf. Intell. Syst. Mol. Biol. (1999) 202-210
    • (1999) Proc. Int. Conf. Intell. Syst. Mol. Biol. , pp. 202-210
    • Myers, G.1
  • 120
    • 2042437650 scopus 로고    scopus 로고
    • Initial sequencing and analysis of the human genome
    • Lander E.S., et al. Initial sequencing and analysis of the human genome. Nature 409 6822 (2001) 860-921
    • (2001) Nature , vol.409 , Issue.6822 , pp. 860-921
    • Lander, E.S.1
  • 121
    • 0037934515 scopus 로고    scopus 로고
    • End-sequence profiling: Sequence-based analysis of aberrant genomes
    • Volik S., et al. End-sequence profiling: Sequence-based analysis of aberrant genomes. Proc. Natl. Acad. Sci. USA (2003)
    • (2003) Proc. Natl. Acad. Sci. USA
    • Volik, S.1
  • 122
    • 0031669184 scopus 로고    scopus 로고
    • Overlapping genomic sequences: a treasure trove of single-nucleotide polymorphisms
    • Taillon-Miller P., et al. Overlapping genomic sequences: a treasure trove of single-nucleotide polymorphisms. Genome Res. 8 7 (1998) 748-754
    • (1998) Genome Res. , vol.8 , Issue.7 , pp. 748-754
    • Taillon-Miller, P.1
  • 123
    • 0034727107 scopus 로고    scopus 로고
    • An SNP map of the human genome generated by reduced representation shotgun sequencing
    • Altshuler D., et al. An SNP map of the human genome generated by reduced representation shotgun sequencing. Nature 407 6803 (2000) 513-516
    • (2000) Nature , vol.407 , Issue.6803 , pp. 513-516
    • Altshuler, D.1
  • 124
    • 17344380534 scopus 로고    scopus 로고
    • An SNP map of human chromosome 22
    • Mullikin J.C., et al. An SNP map of human chromosome 22. Nature 407 6803 (2000) 516-520
    • (2000) Nature , vol.407 , Issue.6803 , pp. 516-520
    • Mullikin, J.C.1
  • 125
    • 17744396306 scopus 로고    scopus 로고
    • A SNP resource for human chromosome 22: extracting dense clusters of SNPs from the genomic sequence
    • Dawson E., et al. A SNP resource for human chromosome 22: extracting dense clusters of SNPs from the genomic sequence. Genome Res. 11 1 (2001) 170-178
    • (2001) Genome Res. , vol.11 , Issue.1 , pp. 170-178
    • Dawson, E.1
  • 126
    • 0037077108 scopus 로고    scopus 로고
    • Comparative genome sequencing for discovery of novel polymorphisms in Bacillus anthracis
    • Read T.D., et al. Comparative genome sequencing for discovery of novel polymorphisms in Bacillus anthracis. Science 296 5575 (2002) 2028-2033
    • (2002) Science , vol.296 , Issue.5575 , pp. 2028-2033
    • Read, T.D.1
  • 128
    • 0036514657 scopus 로고    scopus 로고
    • Algorithmic strategies for the single nucleotide polymorphism haplotype assembly problem
    • Lippert R., et al. Algorithmic strategies for the single nucleotide polymorphism haplotype assembly problem. Briefings in Bioinformatics 3 1 (2002) 23-31
    • (2002) Briefings in Bioinformatics , vol.3 , Issue.1 , pp. 23-31
    • Lippert, R.1
  • 129
    • 0346605568 scopus 로고    scopus 로고
    • Efficiently detecting polymorphisms during the fragment assembly process
    • Fasulo D., et al. Efficiently detecting polymorphisms during the fragment assembly process. Bioinformatics 18 Suppl.1 (2002) S294-S302
    • (2002) Bioinformatics , vol.18 , Issue.SUPPL.1
    • Fasulo, D.1
  • 130
    • 0033975239 scopus 로고    scopus 로고
    • A bacterial genome in flux: the twelve linear and nine circular extrachromosomal DNAs in an infectious isolate of the Lyme disease spirochete Borrelia burgdorferi
    • Casjens S., et al. A bacterial genome in flux: the twelve linear and nine circular extrachromosomal DNAs in an infectious isolate of the Lyme disease spirochete Borrelia burgdorferi. Mol. Microbiol. 35 3 (2000) 490-516
    • (2000) Mol. Microbiol. , vol.35 , Issue.3 , pp. 490-516
    • Casjens, S.1
  • 131
    • 0037033979 scopus 로고    scopus 로고
    • Unsuspected diversity among marine aerobic anoxygenic phototrophs
    • Beja O., et al. Unsuspected diversity among marine aerobic anoxygenic phototrophs. Nature 415 6872 (2002) 630-633
    • (2002) Nature , vol.415 , Issue.6872 , pp. 630-633
    • Beja, O.1
  • 132
    • 0036211215 scopus 로고    scopus 로고
    • Diversity, dynamics, and activity of bacterial communities during production of an artisanal Sicilian cheese as evaluated by 16S rRNA analysis
    • Randazzo C.L., et al. Diversity, dynamics, and activity of bacterial communities during production of an artisanal Sicilian cheese as evaluated by 16S rRNA analysis. Appl. Environ. Microbiol. 68 4 (2002) 1882-1892
    • (2002) Appl. Environ. Microbiol. , vol.68 , Issue.4 , pp. 1882-1892
    • Randazzo, C.L.1
  • 134
    • 77956741168 scopus 로고    scopus 로고
    • Genome pioneer sets sights on Sargasso Sea
    • Whitfield J. Genome pioneer sets sights on Sargasso Sea. Nature Science Update (2003)
    • (2003) Nature Science Update
    • Whitfield, J.1
  • 136
    • 0034666168 scopus 로고    scopus 로고
    • An optimized protocol for analysis of EST sequences
    • Liang F., et al. An optimized protocol for analysis of EST sequences. Nucleic Acids Res. 28 18 (2000) 3657-3665
    • (2000) Nucleic Acids Res. , vol.28 , Issue.18 , pp. 3657-3665
    • Liang, F.1


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