An intermediate grade of finished genomic sequence suitable for comparative analyses

Genome Research

Volumn 14, Issue 11, 2004, Pages 2235-2244

  Blakesley, Robert W ^a   Hansen, Nancy F ^a   Mullikin, James C ^a   Thomas, Pamela J ^a   McDowell, Jennifer C ^a   Maskeri, Baishali ^a   Young, Alice C ^a   Benjamin, Beatrice ^a   Brooks, Shelise Y ^a   Coleman, Bradley I ^a   Gupta, Jyoti ^a   Ho, Shi Ling ^a   Karlins, Eric M ^a   Maduro, Quino L ^a   Stantripop, Sirintorn ^a   Tsurgeon, Cyrus ^a   Vogt, Jennifer L ^a   Walker, Michael A ^a   Masiello, Catherine A ^a   Guan, Xiaobin ^a   Bouffard, Gerard G ^a   Green, Eric D ^a   more..

^a NATIONAL HUMAN GENOME RESEARCH INSTITUTE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; BACTERIAL ARTIFICIAL CHROMOSOME; CLONE; CONTROLLED STUDY; GENE SEQUENCE; HUMAN; HUMAN GENOME; NONHUMAN; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; SEQUENCE HOMOLOGY;

ANIMALS; BASE SEQUENCE; CHROMOSOMES, ARTIFICIAL, BACTERIAL; CLONING, MOLECULAR; COMPUTATIONAL BIOLOGY; CONTIG MAPPING; COSTS AND COST ANALYSIS; DATABASES, GENETIC; EXONS; GENOME; LEMUR; MOLECULAR SEQUENCE DATA; PAPIO; RATS; REPETITIVE SEQUENCES, NUCLEIC ACID; SEQUENCE ANALYSIS, DNA; SEQUENCE HOMOLOGY, NUCLEIC ACID; SOFTWARE;

BACTERIA (MICROORGANISMS);

EID: 7444259980     PISSN: 10889051     EISSN: None     Source Type: Journal    
DOI: 10.1101/gr.2648404     Document Type: Article

References (50)

1. Adams, M.D., Celniker, S.E., Holt, R.A., Evans, C.A., Gocayne, J.D., Amanatides, P.G., Scherer, S.E., Li, P.W., Hoskins, R.A., Galle, R.F., et al. 2000. The genome sequence of Drosophila melanogaster. Science 287: 2185-2195.
2. Aparicio, S., Chapman, J., Stupka, E., Putnam, N., Chia, J,, Dehal, P., Christoffels, A., Rash, S., Hoon, S., Smit, A., et al. 2002. Whole-genome shotgun assembly and analysis of the genome of Fugu rubripes. Science 297: 1301-1310.
3. Ashurst, J.L. and Collins, J.E. 2003. Gene annotation: Prediction and testing. Annu. Rev. Genomics Hum. Genet. 4: 69-88.
4. Bailey, J.A., Gu, Z., Clark, R.A., Reinert, K., Samonte, R.V., Schwartz, S., Adams, M.D., Myers, E.W., Li, P.W., and Eichler, E.E. 2002. Recent segmental duplications in the human genome. Science 297: 1003-1007.
5. Bailey, J.A., Church, D.M., Ventura, M., Rocchi, M., and Eichler, E.E. 2004. Analysis of segmental duplications and genome assembly in the mouse. Genome Res. 14: 789-801.
6. Birren, B., Mancino, V., and Shizuya, H. 1998. Bacterial artificial chromosomes. In Genome analysis: a laboratory manual: Cloning systems, vol. 3 (eds. B. Birren et al.), pp. 241-295. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.
7. Bouck, J., Miller, W., Gorrell, J.H., Muzny, D., and Gibbs, R.A. 1998. Analysis of the quality and utility of random shotgun sequencing at low redundancies. Genome Res. 8: 1074-1084.
8. Burge, C. and Karlin, S. 1997. Prediction of complete gene structures in human genomic DNA. J. Mol. Biol. 268: 78-94.
9. C. elegans Sequencing Consortium. 1998. Genome sequence of the nematode C. elegans: A platform for investigating biology. Science 282: 2012-2018.
10. Chissoe, S.L., Marra, M.A., Hillier, L., Brinkman, R., Wilson, R.K., and Waterston, R.H. 1997. Representation of cloned genomic sequences in two sequencing vectors: Correlation of DNA sequence and subclone distribution. Nucleic Acids Res. 25: 2960-2966.
11. Cooper, G.M. and Sidow, A. 2003. Genomic regulatory regions: Insights from comparative sequence analysis. Curr. Opin. Genet. Dev. 13: 604-610.
12. DeSilva, U., Elnitski, L., Idol, J.R., Doyle, J.L., Gan, W., Thomas, J.W., Schwartz, S., Dietrich, N.L., Beckstrom-Sternberg, S.M., McDowell, J.C., et al. 2002. Generation and comparative analysis of -e13.3 Mb of mouse genomic sequence orthologous to the region of human chromosome 7q11.23 implicated in Williams syndrome. Genome Res. 12: 3-15.
13. Ellsworth, R.E., Jamison, D.C., Touchman, J.W., Chissoe, S.L., Braden Maduro, V.V., Bouffard, G.G., Dietrich, N.L., Beckstrom-Sternberg, S.M., Iyer, L.M., Weintraub, L.A., et al. 2000. Comparative genomic sequence analysis of the human and mouse cystic fibrosis transmembrane conductance regulator genes. Proc. Natl. Acad. Sci. 97: 1172-1177.
14. Ewing, B. and Green, P. 1998. Base-calling of automated sequencer traces using Phred. II. Error probabilities. Genome Res. 8: 186-194.
15. Ewing, B., Hillier, L., Wendl, M.C., and Green, P. 1998. Base-calling of automated sequencer traces using Phred. I: Accuracy assessment. Genome Res. 8: 175-185.
16. Felsenfeld, A., Peterson, J., Schloss, J., and Guyer, M. 1999. Assessing the quality of the DNA sequence from the Human Genome Project. Genome Res. 9: 1-4.
17. Frazer, K.A., Elnitski, L., Church, D.M., Dubchak, I., and Hardison, R.C. 2003. Cross-species sequence comparisons: A review of methods and available resources. Genome Res. 13: 1-12.
18. Gordon, D., Abajian, C., and Green, P. 1998. Consed: A graphical tool for sequence finishing. Genome Res. 8: 195-202.
19. Gordon, D., Desmarais, C., and Green, P. 2001. Automated finishing with Autofinish. Genome Res. 11: 614-625.
20. Green, F.D. 2001. Strategies for the systematic sequencing of complex genomes. Nat. Rev. Genet. 2: 573-583.
21. Hite, J.M., Eckert, K.A., and Cheng, K.C. 1996. Factors affecting fidelity of DNA synthesis during PCR amplification of d(C-A)n.d(G-T)n microsatellite repeats. Nucleic Acids Res. 24: 2429-2434.
22. International Human Genome Sequencing Consortium. 2001. Initial sequencing and analysis of the human genome. Nature 409: 860-921.
23. International Human Genome Sequencing Consortium. 2004. Finishing the euchromatic sequence of the human genome. Nature (in press).
24. Ishiura, M., Hazumi, N., Koide, T., Uchida, T., and Okada, Y. 1989. A recB recC sbcB recJ host prevents recA-independent deletions in recombinant cosmid DNA propagated in Escherichia coli. J. Bacteriol. 171: 1068-1074.
25. Istrail, S., Sutton, G.G., Florea, L., Halpern, A.L., Mobarry, C.M., Lippert, R., Walenz, B., Shatkay, H., Dew, I., Miller, J.R., et al. 2004. Whole-genome shotgun assembly and comparison of human genome assemblies. Proc. Natl. Acad. Sci. 101: 1916-1921.
26. Keith, J.M., Cochran, D.A.E., Lala, G.H., Adams, P., Bryant, D., and Mitchelson, K.R. 2004. Unlocking hidden genomic sequence. Nucleic Acids Res. 32: e35.
27. Langan, J.E., Rowbottom, L., Liloglou, T., Field, J.K., and Risk, J.M. 2002. Sequencing of difficult templates containing poly(A/T) tracts: Closure of sequence gaps. BioTechniques 33: 276-280.
28. Margulies, E.H., NISC Comparative Sequencing Program, and Green, E.D. 2003a. Detecting highly conserved regions of the human genome by multispecies sequence comparisons. Cold Spring Harbor Symp. Quant. Biol. LXVIII: 255-263.
29. Margulies, E.H., Blanchette, M., NISC Comparative Sequencing Program, Haussler, D., and Green, E.D. 2003b. Identification and characterization of multi-species conserved sequences. Genome Res. 13: 2507-2518.
30. McMurray, A.A., Sulston, J.E., and Quail, M.A. 1998. Short-insert libraries as a method of problem solving in genome sequencing. Genome Res. 8: 562-566.
31. Miller, W., Makova, K.D., Nekrutenko, A., and Hardison, R.C. 2004. Comparative Genomics. Annu. Rev. Genomics Hum. Genet. 5: 15-56.
32. Mouse Genome Sequencing Consortium. 2002. Initial sequencing and comparative analysis of the mouse genome. Nature 420: 520-562.
33. Mytelka, D.S. and Chamberlin, M.J. 1996. Analysis and suppression of DNA polymerase pauses associated with a trinucleotide consensus. Nucleic Acids Res. 24: 2774-2781.
34. Ning, Z., Cox, A.J., and Mullikin, J.C. 2001. SSAHA: A fast search method for large DNA databases. Genome Res. 11: 1725-1729.
35. Nobrega, M.A. and Pennacchio, L.A. 2004. Comparative genomic analysis as a tool for biological discovery. J. Physiol. 554: 31-39.
36. Palmer, L.E. and McCombie, W.R. 2002. On the importance of being finished. Genome Biol. 3: 2010.1-2010.4
37. Pennacchio, L.A. and Rubin, E.M. 2003. Comparative genomic tools and databases: Providing insights into the human genome. J. Clin. Invest. 111: 1099-1106.
38. Rat Genome Sequencing Project Consortium. 2004. Genome sequence of the Brown Norway rat yields insights into mammalian evolution. Nature 428: 493-521.
39. Razin, S.V., Ioudinkova, E.S., Trifonov, E.N., and Scherrer, K. 2001. Non-clonability correlates with genomic instability: A case study of a unique DNA region. J. Mol. Biol. 307: 481-486.
40. Sanger, F., Coulson, A.R., Hong, G.F., Hill, D.F., and Petersen, G.B. 1982. Nucleotide sequence of the bacteriophage λ DNA. J. Mol. Biol. 162: 729-773.
41. Schwartz, S., Zhang, Z., Frazer, K.A., Smit, A., Riemer, C., Bouck, J., Gibbs, R., Hardison, R., and Miller, W. 2000. PipMaker: A web server for aligning two genomic DNA sequences. Genome Res. 10: 577-586.
42. Schwartz, S., Elnitski, L., Li, M., Weirauch, M., Riemer, C., Smit, A., NISC Comparative Sequencing Program, Green, E.D., Hardison, R.C., and Miller, W. 2003. MultiPipMaker and supporting tools: Alignments and analysis of multiple genomic DNA sequences. Nucleic Acids Res. 31: 3518-3524.
43. Shizuya, H., Birren, B., Kim, U.-J., Mancino, V., Slepak, T., Tachiiri, Y., and Simon, M. 1992. Cloning and stable maintenance of 300-kilobase-pair fragments of human DNA in Escherichia coli using an F-factor-based vector. Proc. Natl. Acad. Sci. 89: 8794-8797.
44. Stajich, J.E., Block, D., Boulez, K., Brenner, S.E., Chervitz, S.A., Dagdigian, C., Fuellen, G., Gilbert, J.G., Korf, I., Lapp, H., et al. 2002. The Bioperl toolkit: Perl modules for the life sciences. Genome Res. 12: 1611-1618.
45. Stein, L. 2001. Genome annotation: From sequence to biology. Nat. Rev. Genet. 2: 493-503.
46. Stein, L.D., Bao, Z., Blasiar, D., Blumenthal, T., Brent, M.R., Chen, N., Chinwalla, A., Clarke, L., Clee, C., Coghlan, A., et al. 2003. The genome sequence of Caenorhabditis briggsae: A platform for comparative genomics. PLoS. Biol. 1: 166-192.
47. Thomas, J.W., Touchman, J.W., Blakesley, R.W., Bouffard, G.G., Beckstrom-Sternberg, S.M., Margulies, E.H., Blanchette, M., Siepel, A.C., Thomas, P.J., McDowell, J.C., et al. 2003. Comparative analyses of multi-species sequences from targeted genomic regions. Nature 424: 788-793.
48. Venter, J.C., Adams, M.D., Myers, E.W., Li, P.W., Mural, R.J., Sutton, G.G., Smith, H.O., Yandell, M., Evans, C.A., Holt, R.A., et al. 2001. The sequence of the human genome. Science 291: 1304-1351.
49. Wilson, R.K. and Mardis, E.R. 1997a. Fluorescence-based DNA sequencing. In Genome analysis: A laboratory manual: Analyzing DNA, vol. 1 (eds. B. Birren et al.), pp. 301-395. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.
50. Wilson, R.K. and Mardis, E.R. 1997b. Shotgun sequencing. In Genome analysis: A laboratory manual: Analyzing DNA, vol. 1 (eds. B. Birren et al.), pp. 397-454. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.