An effective approach for analyzing 'prefinished' genomic sequence data

Genome Research

Volumn 9, Issue 2, 1999, Pages 189-194

  Kuehl, Peter M ^a,b,c   Weisemann, Jane M ^c   Touchman, Jeffrey W ^b   Green, Eric D ^b   Boguski, Mark S ^c  

^a UNIVERSITY OF MARYLAND   (United States)

^b NATIONAL HUMAN GENOME RESEARCH INSTITUTE   (United States)

^c NATIONAL INSTITUTES OF HEALTH   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CONTIG;

ARTICLE; CHROMOSOME 7; COMPUTER PROGRAM; DATA BASE; GENE SEQUENCE; GENETIC ANALYSIS; PRIORITY JOURNAL;

ALGORITHMS; BASE SEQUENCE; DATABASES, FACTUAL; DNA; GENOME, HUMAN; HUMANS; INTERNET; SEQUENCE ANALYSIS, DNA; SOFTWARE;

EID: 0033020427     PISSN: 10889051     EISSN: None     Source Type: Journal    
DOI: None     Document Type: Article

References (25)

1. Altschul, S.F., M.S. Boguski, W. Gish, and J.C. Wootton. 1994. Issues in searching molecular sequence databases. Nature Genet. 6: 119.
2. Benson, D.A., M.S. Boguski, D.J. Lipman, J. Ostell, and B.F.F. Ouellette. 1998. GenBank. Nucleic Acids Res. 26: 1-7.
3. Boguski, M., A. Chakravarti, R. Gibbs, E. Green, and R.M. Myers. 1996. The end of the beginning: The race to begin human genome sequencing. Genome Res. 6: 771-772.
4. Burge, C. and S. Karlin. 1997. Prediction of complete gene structures in human genomic DNA. J. Mol. Riol. 268: 78-94.
5. Chao, K.M., J. Zhang, J. Ostell, and W. Miller. 1995. A local alignment tool for very long DNA sequences. Comput. Appl. Biosci. 11: 147-153.
6. Collins, F.S., A. Patrinos, E. Jordan, A. Chakravarti, R. Gesteland, and L. Walters. 1998. New goals for the U.S. Human Genome Project: 1998-2003. Science 282: 682-689.
7. Ewing, B. and P. Green. 1998. Base-calling of automated sequencer traces using Phred. II. Error probabilities. Genome Res. 8: 186-194.
8. Ewing, B., L. Hillier, M.C. Wendl, and P. Green. 1998. Base-calling of automated sequencer traces using Phred. I. Accuracy assessment. Genome Res. 8: 175-185.
9. Gordon, D., C. Abajian, and P. Green. 1998. Consed: A graphical tool for sequence finishing. Genome Res. 8: 195-202.
10. Green, P. 1997. Against a whole-genome shotgun. Genome Res. 7: 410-417.
11. Kans, J.A. and B.F.F. Ouellette. 1998. Submitting DNA sequence to the databases. In Bioinformatics: A practical guide to the analysis of genes and proteins (ed. A.D. Baxevanis and B.F.F. Ouellette), pp. 318-353. John Wiley and Sons, New York, NY.
12. Olson, M.V. 1995. A time to sequence. Science 270: 394-396.
13. Ostell, J.M. and J.A. Kans. 1998. The NCBI data model. In Bioinformatics: A practical guide to the analysis of genes and proteins (ed. A.D. Baxevanis and B.F.F. Ouellette), pp. 121-144. John Wiley and Sons, New York, NY.
14. Ouellette, B.F.F. and M.S. Boguski. 1997. Database divisions and homology search files: A guide for the perplexed. Genome Res. 7: 952-955.
15. Pruitt, K.D. 1997. Webwise: Navigating the human genome project. Genome Res. 7: 1038-1039.
16. Schuler, G.D., M.S. Boguski, E.A. Stewart, L.D. Stein, G. Gyapay, K. Rice, R.E. White, P. Rodriguez-Tome, A. Aggarwal, E. Bajorek et al. 1996. A gene map of the human genome. Science 274: 540-546.
17. Statement on the rapid release of genomic DNA sequence. 1998. Genome Res. 8: 413.
18. Venter, J.C., M.D. Adams, G.G. Sutton, A.R. Kerlavage, H.O. Smith, and M. Hunkapiller. 1998. Shotgun sequencing of the human genome. Science 280: 1540-1542.
19. Weber, J.L. and E.W. Myers. 1997. Human whole-genome shotgun sequencing. Genome Res. 7: 401-409.
20. Wheelan, S.J. and M.S. Boguski. 1998. Late-night thoughts on the sequence annotation problem. Genome Res. 8: 168-169.
21. Wilson, R.K. and E.R. Mardis. 1997. Shotgun sequencing. In Genome analysis: A laboratory manual. Vol. 1 Analyzing DNA (ed. B. Birren et al.), pp. 397-454. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.
22. Wooton, J.C. and S. Federhen. 1996. Analysis of compositionally biased regions in sequence databases. Methods Enzymol. 266: 554-571.
23. Xu, Y., R. Mural, M. Shah, and E. Uberbacher. 1994. Recognizing exons in genomic sequence using GRAIL II. Genet. Eng. 16: 241-253.
24. Zhang, J. and T.L. Madden. 1997. PowerBLAST: A new network BLAST application for interactive or automated sequence analysis and annotation. Genome Res. 7: 649-656.
25. Zhang, M.Q. 1997. Identification of protein coding regions in the human genome by quadratic discriminant analysis. Proc. Natl. Acad. Sci. 94: 565-568.