-
1
-
-
0025183708
-
A basic local alignment search tool
-
ALTSCHUL, S.,W. GISH, W.MILLER, E. MYERS AND D. LIPMAN. 1990. A basic local alignment search tool. J. Mol. Biol. 215: 403-10.
-
(1990)
J. Mol. Biol.
, vol.215
, pp. 403-410
-
-
Altschul, S.1
Gish, W.2
Miller, W.3
Myers, E.4
Lipman, D.5
-
2
-
-
0030833564
-
Realigner: a program for refining DNA sequence multialignments
-
ANSON, E. AND E. MYERS. 1997. Realigner: a program for refining DNA sequence multialignments. J. Comput. Biol. 4: 369-83.
-
(1997)
J. Comput. Biol.
, vol.4
, pp. 369-383
-
-
Anson, E.1
Myers, E.2
-
3
-
-
0037162885
-
Whole-genome shotgun assembly and analysis of the genome of Fugu rubripes
-
APARICIO, S., J. CHAPMAN, E. STUPKA et al. 2002. Whole-genome shotgun assembly and analysis of the genome of Fugu rubripes. Science 297: 1301-10.
-
(2002)
Science
, vol.297
, pp. 1301-1310
-
-
Aparicio, S.1
Chapman, J.2
Stupka, E.3
-
4
-
-
0036144823
-
ARACHNE: a whole genome shotgun assembler
-
BATZOGLOU, S., D.B. JAFFE, K. STANLEY, et al. 2002. ARACHNE: a whole genome shotgun assembler. Genome Res. 12: 177-89.
-
(2002)
Genome Res.
, vol.12
, pp. 177-189
-
-
Batzoglou, S.1
Jaffe, D.B.2
Stanley, K.3
-
5
-
-
0032644644
-
q-gram based database searching using suffix arrays
-
BURKHARDT, S., A. CRAUSER, P. FERRAGINA, H.-P. LENHOF, E. RIVALS AND M. VINGRON. 1999. q-gram based database searching using suffix arrays. Proc. RECOMB 3: 77-83.
-
(1999)
Proc. RECOMB
, vol.3
, pp. 77-83
-
-
Burkhardt, S.1
Crauser, A.2
Ferragina, P.3
Lenhof, H.-P.4
Rivals, E.5
Vingron, M.6
-
6
-
-
0028516811
-
Sublinear approximate string matching
-
CHANG, W. AND E. LAWLER. 1994. Sublinear approximate string matching. Algorithmica 12: 327-44.
-
(1994)
Algorithmica
, vol.12
, pp. 327-344
-
-
Chang, W.1
Lawler, E.2
-
7
-
-
0026693729
-
Aligning two sequences within a specified diagonal band
-
CHAO, K.,W. PEARSON AND W. MILLER. 1992. Aligning two sequences within a specified diagonal band. Comput. App. Biosci. 8: 481-7.
-
(1992)
Comput. App. Biosci.
, vol.8
, pp. 481-487
-
-
Chao, K.1
Pearson, W.2
Miller, W.3
-
8
-
-
0242266906
-
Barnacle: an assembly algorithm for clone-based sequences of whole genomes
-
CHOI, V. AND M. FARACH-COLTON. 2003. Barnacle: an assembly algorithm for clone-based sequences of whole genomes. Gene 320: 165-76.
-
(2003)
Gene
, vol.320
, pp. 165-176
-
-
Choi, V.1
Farach-Colton, M.2
-
9
-
-
0026753344
-
The accuracy of DNA sequences: estimating sequence quality
-
CHURCHILL, G. AND M. S. WATERMAN. 1992. The accuracy of DNA sequences: estimating sequence quality. Genomics 14: 89-98.
-
(1992)
Genomics
, vol.14
, pp. 89-98
-
-
Churchill, G.1
Waterman, M.S.2
-
10
-
-
2242464840
-
The draft genome of Ciona intestinalis: insights into chordate and vertebrate origins
-
DEHAL, P., Y. SATOU, R. CAMPBELL, et al. 2002/2003. The draft genome of Ciona intestinalis: insights into chordate and vertebrate origins. Science 298: 2157-68.
-
(2002)
Science
, vol.298
, pp. 2157-2168
-
-
Dehal, P.1
Satou, Y.2
Campbell, R.3
-
11
-
-
0036444801
-
Map error reduction: using genetic and sequence-based physical maps to order closely linked markers
-
DEWAN, A.,A. PARRADO AND T. MATISE. 2002. Map error reduction: using genetic and sequence-based physical maps to order closely linked markers. Human Hered. 54: 34-44.
-
(2002)
Human Hered.
, vol.54
, pp. 34-44
-
-
Dewan, A.1
Parrado, A.2
Matise, T.3
-
12
-
-
0031955518
-
Base-calling of automated sequencer traces using phred. I. Accuracy assessment
-
EWING, B., L. HILLIER, M.WENDL AND P. GREEN. 1998. Base-calling of automated sequencer traces using phred. I. Accuracy assessment. Genome Res. 8: 175-85.
-
(1998)
Genome Res.
, vol.8
, pp. 175-185
-
-
Ewing, B.1
Hillier, L.2
Wendl, M.3
Green, P.4
-
13
-
-
0031978181
-
Basecalling of automated sequencer traces using phred. II. Error probabilities
-
EWING, B. AND P. GREEN. 1998. Basecalling of automated sequencer traces using phred. II. Error probabilities. Genome Res. 8: 186-94.
-
(1998)
Genome Res.
, vol.8
, pp. 186-194
-
-
Ewing, B.1
Green, P.2
-
14
-
-
0029653518
-
Whole-genome random sequencing and assembly of Haemophilus influenzae
-
FLEISCHMANN, R. D.,M. ADAMS, O. WHITE, et al. 1995. Whole-genome random sequencing and assembly of Haemophilus influenzae. Science 26: 496-512.
-
(1995)
Science
, vol.26
, pp. 496-512
-
-
Fleischmann, R.D.1
Adams, M.2
White, O.3
-
16
-
-
0008068437
-
PHRAP documentation
-
GREEN, P. 1994. PHRAP documentation. http: //www.phrap.org.
-
(1994)
-
-
Green, P.1
-
17
-
-
0030972827
-
Against a whole-genome shotgun
-
GREEN, P. 1997. Against a whole-genome shotgun. Genome Res. 7: 410-7.
-
(1997)
Genome Res.
, vol.7
, pp. 410-417
-
-
Green, P.1
-
18
-
-
1842717960
-
The Atlas genome assembly system
-
HAVLAK, P., R. CHEN, K. DURBIN, A. EGAN, Y. REN, X.-Z. SONG, G. WEINSTOCK AND R. GIBBS. 2004. The Atlas genome assembly system. Genome Res. 14: 721-32.
-
(2004)
Genome Res.
, vol.14
, pp. 721-732
-
-
Havlak, P.1
Chen, R.2
Durbin, K.3
Egan, A.4
Yre, N.5
Song, X.-Z.6
Weinstock, G.7
Gibbs, R.8
-
19
-
-
84889864300
-
A whole-genome assembly of Drosophila
-
HOLT, R. A., G.M. SUBRAMANIAN, A. HALPER, et al. 2002. A whole-genome assembly of Drosophila. Science 288: 129-49.
-
(2002)
Science
, vol.288
, pp. 129-149
-
-
Holt, R.A.1
Subramanian, G.M.2
Halper, A.3
-
20
-
-
0141853948
-
PCAP: a whole-genome assembly program
-
HUANG, X., J.WANG, S. ALURU, S.-P. YANG AND L. HILLIER. 2003. PCAP: a whole-genome assembly program. Genome Res. 13: 2164-70.
-
(2003)
Genome Res.
, vol.13
, pp. 2164-2170
-
-
Huang, X.1
Wang, J.2
Aluru, S.3
Yang, S.-P.4
Hillier, L.5
-
21
-
-
0032849859
-
CAP3: A DNA sequence assembly program
-
HUANG, X. AND A. MADAN. 1999. CAP3: A DNA sequence assembly program. Genome Res. 9: 868-77.
-
(1999)
Genome Res.
, vol.9
, pp. 868-877
-
-
Huang, X.1
Madan, A.2
-
22
-
-
0026693586
-
A contig assembly program based on sensitive detection of fragment overlaps
-
HUANG, X. 1992. A contig assembly program based on sensitive detection of fragment overlaps. Genomics 14: 18-25.
-
(1992)
Genomics
, vol.14
, pp. 18-25
-
-
Huang, X.1
-
23
-
-
1242281253
-
The greedy pathmerging algorithm for contig scaffolding
-
HUSON, D.H., K. REINERT AND E.W. MYERS. 2002. The greedy pathmerging algorithm for contig scaffolding. J. ACM 49: 603-15.
-
(2002)
J. ACM
, vol.49
, pp. 603-615
-
-
Huson, D.H.1
Reinert, K.2
Myers, E.W.3
-
24
-
-
0035224746
-
Design of a compartmentalized shotgun assembler for the human genome
-
HUSON, D.H., K. REINERT, S. A. KRAVITZ, et al. 2001. Design of a compartmentalized shotgun assembler for the human genome. Bioinformatics 17: 132-9.
-
(2001)
Bioinformatics
, vol.17
, pp. 132-139
-
-
Huson, D.H.1
Reinert, K.2
Kravitz, S.A.3
-
25
-
-
2042437650
-
Initial sequencing and analysis of the human genome
-
International Human Genome Sequencing Consortium
-
INTERNATIONAL HUMAN GENOME SEQUENCING CONSORTIUM. 2001. Initial sequencing and analysis of the human genome. Nature 409: 860-921.
-
(2001)
Nature
, vol.409
, pp. 860-921
-
-
-
26
-
-
0037267048
-
Whole-genome sequence assembly for mammalian genomes: ARACHNE 2
-
JAFFE, D., J. BUTLER, S. GNERRE, et al. 2003. Whole-genome sequence assembly for mammalian genomes: ARACHNE 2. Genome Res. 13: 91-6.
-
(2003)
Genome Res.
, vol.13
, pp. 91-96
-
-
Jaffe, D.1
Butler, J.2
Gnerre, S.3
-
27
-
-
0037267048
-
Whole genome sequence assembly for mammalian genomes: ARACHNE 2
-
JAFFE, D., J. BUTLER, S. GNERRE, et al. 2003. Whole genome sequence assembly for mammalian genomes: ARACHNE 2. Genome Res. 13: 91-6.
-
(2003)
Genome Res.
, vol.13
, pp. 91-96
-
-
Jaffe, D.1
Butler, J.2
Gnerre, S.3
-
28
-
-
0034819969
-
Separating repeats in DNA sequence assembly
-
KECECIOGLU, J. AND J. YU. 2001. Separating repeats in DNA sequence assembly. Proc. RECOMB 5: 176-83.
-
(2001)
Proc. RECOMB
, vol.5
, pp. 176-183
-
-
Kececioglu, J.1
Yu, J.2
-
29
-
-
0034837599
-
Assembly of the working draft of the human genome with GigAssembler
-
KENT, W. J. AND D. HAUSSLER. 2001. Assembly of the working draft of the human genome with GigAssembler. Genome Res. 11: 1541-8.
-
(2001)
Genome Res.
, vol.11
, pp. 1541-1548
-
-
Kent, W.J.1
Haussler, D.2
-
30
-
-
0003795553
-
The Code of Codes: Scientific and Social Issues in the Human Genome Project
-
Harvard University Press, Cambridge, MA
-
KEVLES, D. J. AND L. HOOD. 1992. The Code of Codes: Scientific and Social Issues in the Human Genome Project. Harvard University Press, Cambridge, MA.
-
(1992)
-
-
Kevles, D.J.1
Hood, L..2
-
31
-
-
0023988195
-
Genomic mapping by fingerprinting random clones: a mathematical analysis
-
LANDER, E. S. AND M. S. WATERMAN. 1988. Genomic mapping by fingerprinting random clones: a mathematical analysis. Genomics 2: 231-9.
-
(1988)
Genomics
, vol.2
, pp. 231-239
-
-
Lander, E.S.1
Waterman, M.S.2
-
32
-
-
0031599976
-
Expressed sequence tags - ESTablishing bridges between genomes
-
MARRA, M., L. HILLIER AND R. H. WATERSTON. 1998. Expressed sequence tags - ESTablishing bridges between genomes. Trends Genet. 14: 4-7.
-
(1998)
Trends Genet.
, vol.14
, pp. 4-7
-
-
Marra, M.1
Hillier, L.2
Waterston, R.H.3
-
33
-
-
0033824409
-
Automation for genomics, part 1: preparation for sequencing
-
MELDRUM, D. 2000. Automation for genomics, part 1: preparation for sequencing. Genome Res. 10: 1081-92.
-
(2000)
Genome Res.
, vol.10
, pp. 1081-1092
-
-
Meldrum, D.1
-
34
-
-
0033804353
-
Automation for genomics, part 2: sequencers, microarrays, and future trends
-
MELDRUM, D. 2000. Automation for genomics, part 2: sequencers, microarrays, and future trends. Genome Res. 10: 1288-303.
-
(2000)
Genome Res.
, vol.10
, pp. 1288-1303
-
-
Meldrum, D.1
-
35
-
-
8544240102
-
An overview of the yeast genome
-
MEWES, W., K. ALBERMANN, M. BÄHR, et al. 1997. An overview of the yeast genome. Nature 387: 7-8.
-
(1997)
Nature
, vol.387
, pp. 7-8
-
-
Mewes, W.1
Albermann, K.2
Bähr, M.3
-
36
-
-
0037263854
-
The Phusion assembler
-
MULLIKIN, J. AND Z. NING. 2003. The Phusion assembler. Genome Res. 13: 81-90.
-
(2003)
Genome Res.
, vol.13
, pp. 81-90
-
-
Mullikin, J.1
Ning, Z.2
-
37
-
-
0037204994
-
A comparison of whole-genome shotgun-derived mouse chromosome 16 and the human genome
-
MURAL, R. J.,M.D. ADAMS, G.W. MYERS, et al. 2002. A comparison of whole-genome shotgun-derived mouse chromosome 16 and the human genome. Science 296: 1661-71.
-
(2002)
Science
, vol.296
, pp. 1661-1671
-
-
Mural, R.J.1
Adams, M.D.2
Myers, G.W.3
-
38
-
-
0034708758
-
A wholegenome assembly of Drosophila
-
MYERS, E.W., G. G. SUTTON, A. L. DELCHER, et al. 2000. A wholegenome assembly of Drosophila. Science 287: 2196-204.
-
(2000)
Science
, vol.287
, pp. 2196-2204
-
-
Myers, E.W.1
Sutton, G.G.2
Delcher, A.L.3
-
39
-
-
84889872121
-
A fast bit-vector algorithm for approximate string matching based on dynamic programming
-
MYERS, E. 1990. A fast bit-vector algorithm for approximate string matching based on dynamic programming. J. ACM 46: 495-515.
-
(1990)
J. ACM
, vol.46
, pp. 495-515
-
-
Myers, E.1
-
40
-
-
0028516571
-
A sublinear algorithm for approximate keyword matching
-
MYERS, E. 1994. A sublinear algorithm for approximate keyword matching. Algorithmica 12: 345-74.
-
(1994)
Algorithmica
, vol.12
, pp. 345-374
-
-
Myers, E.1
-
41
-
-
0029312158
-
Toward simplifying and accurately formulating fragment assembly
-
MYERS, E. 1995. Toward simplifying and accurately formulating fragment assembly. J. Comput. Biol. 2: 275-90.
-
(1995)
J. Comput. Biol.
, vol.2
, pp. 275-290
-
-
Myers, E.1
-
42
-
-
0023055106
-
Human genome - Department of Energy on the map
-
PALCA, J. 1986. Human genome - Department of Energy on the map. Nature 321: 371.
-
(1986)
Nature
, vol.321
, pp. 371
-
-
Palca, J.1
-
44
-
-
0003921505
-
Computational Molecular Biology
-
MIT Press, Cambridge, MA
-
PEVZNER, P. 2000. Computational Molecular Biology. MIT Press, Cambridge, MA.
-
(2000)
-
-
Pevzner, P.1
-
45
-
-
84859942010
-
Efficient q-gram filters for finding all epsilon-matches over a given length
-
RASMUSSEN, K., J. STOYE AND E.W. MYERS. 2005. Efficient q-gram filters for finding all epsilon-matches over a given length. Proc. RECOMB 9: 189-203.
-
(2005)
Proc. RECOMB
, vol.9
, pp. 189-203
-
-
Rasmussen, K.1
Stoye, J.2
Myers, E.W.3
-
46
-
-
1842684068
-
The genome sequence of the brown Norway rat yields insights into mammalian evolution
-
Rat Genome Sequencing Consortium
-
RAT GENOME SEQUENCING CONSORTIUM. 2004. The genome sequence of the brown Norway rat yields insights into mammalian evolution. Nature 428: 493-521.
-
(2004)
Nature
, vol.428
, pp. 493-521
-
-
-
47
-
-
10244230901
-
A gene map of the human genome
-
SCHULER, G.,M. BOGUSKI, E. STEWART, et al. 1996. A gene map of the human genome. Science 274: 540-6.
-
(1996)
Science
, vol.274
, pp. 540-546
-
-
Schuler, G.1
Boguski, M.2
Stewart, E.3
-
48
-
-
0024756323
-
The Santa Cruz Workshop - May 1985
-
SINSHEIMER, A. L. 1985. The Santa Cruz Workshop - May 1985. Genomics 5: 954-6.
-
(1985)
Genomics
, vol.5
, pp. 954-956
-
-
Sinsheimer, A.L.1
-
49
-
-
84889776510
-
Shotgun fragment assembly
-
Oxford University Press, Oxford: to appear
-
SUTTON, G. AND I. DEW. 2005. Shotgun fragment assembly. In Series in Systems Biology. Oxford University Press, Oxford: to appear.
-
(2005)
Series in Systems Biology
-
-
Sutton, G.1
Dew, I.2
-
50
-
-
0001899550
-
TIGR Assembler: A new tool for assembling large shotgun sequencing projects
-
SUTTON, G.G., O.WHITE, M.D. ADAMS AND A. R. KERLAVAGE. 1995. TIGR Assembler: A new tool for assembling large shotgun sequencing projects. Genome Sci. Technol. 1: 9-19.
-
(1995)
Genome Sci. Technol.
, vol.1
, pp. 9-19
-
-
Sutton, G.G.1
White, O.2
Adams, M.D.3
Kerlavage, A.R.4
-
52
-
-
0036204075
-
Separation of nearly identical repeats in shotgun assemblies using defined nucleotide positions, DNPs
-
TAMMI, M., E. ARNER, T. BRITTON AND B. ANDERSSON. 2002. Separation of nearly identical repeats in shotgun assemblies using defined nucleotide positions, DNPs. Bioinformatics 18: 379-88.
-
(2002)
Bioinformatics
, vol.18
, pp. 379-388
-
-
Tammi, M.1
Arner, E.2
Britton, T.3
Andersson, B.4
-
53
-
-
84889823826
-
-
TIGR, The AMOS web page
-
TIGR. 2005. The AMOS web page, http: //www.tigr.org/software/AMOS.
-
(2005)
-
-
-
54
-
-
0035895505
-
The sequence of the human genome
-
VENTER, J.C.,M.D. ADAMS, E.W. MYERS, et al., 2001. The sequence of the human genome. Science 291: 1145-1434.
-
(2001)
Science
, vol.291
, pp. 1145-1434
-
-
Venter, J.C.1
Adams, M.D.2
Myers, E.W.3
-
55
-
-
18444378733
-
RePS: a sequence assembler that masks exact repeats identified from the shotgun data
-
WANG, J., G.K.-S.WONG, P. NI, et al., 2002. RePS: a sequence assembler that masks exact repeats identified from the shotgun data. Genome Res. 12: 824-31.
-
(2002)
Genome Res.
, vol.12
, pp. 824-831
-
-
Wang, J.1
Wong, G.K.-S.2
Ni, P..3
-
56
-
-
0030950735
-
Human whole-genome shotgun sequencing
-
WEBBER, J.L. AND E.W. MYERS. 1997. Human whole-genome shotgun sequencing. Genome Res. 7: 401-9.
-
(1997)
Genome Res.
, vol.7
, pp. 401-409
-
-
Webber, J.L.1
Myers, E.W.2
-
57
-
-
0037023384
-
A draft sequence of the rice genome (Oryza sative L. ssp. indica)
-
YU, J., S.HU, J. WANG, et al. 2002. A draft sequence of the rice genome (Oryza sative L. ssp. indica). Science 296: 79-92.
-
(2002)
Science
, vol.296
, pp. 79-92
-
-
Yu, J.1
Hu, S.2
Wang, J.3
|