Analysis of the quality and utility of random shotgun sequencing at low redundancies

Genome Research

Volumn 8, Issue 10, 1998, Pages 1074-1084

  Bouck, John ^a   Miller, Webb ^b   Gorrell, James H ^a   Muzny, Donna ^a   Gibbs, Richard A ^a  

^a BAYLOR COLLEGE OF MEDICINE   (United States)

^b The Pennsylvania State University   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DNA;

ARTICLE; CONSENSUS SEQUENCE; DATA BASE; DNA LIBRARY; DNA SEQUENCE; METHODOLOGY; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; SEQUENCE HOMOLOGY;

EID: 0031722856     PISSN: 10889051     EISSN: None     Source Type: Journal    
DOI: 10.1101/gr.8.10.1074     Document Type: Article

References (24)

1. Altschul, S.F., W. Gish, W. Miller, E.W. Myers, and D.J. Lipman. 1990. Basic local alignment search tool. J. Mol. Biol. 215: 403-410.
2. Ansari-Lari, M.A., D.M. Muzny, J. Lu, F. Lu, C.E. Lilley, S. Spanos, T. Malley, and R.A. Gibbs. 1996. A gene-rich cluster between the CD4 and triosephosphate isomerase genes at human chromosome 12p13. Genome Res. 6: 314-326.
3. Ansari-Lari, M.A., Y. Shen, D.M. Muzny, W. Lee, and R.A. Gibbs. 1997. Large-scale sequencing in human chromosome 12p13: Experimental and computational gene structure determination. Genome Res. 7: 268-280.
4. Ansari-Lari, M.A., J.C. Oeltjen, S. Schwartz, Z. Zhang, D.M. Muzny, J. Lu, J.H. Gorrell, A.C. Chinault, J.W. Belmont, W. Miller, and R.A. Gibbs. 1998. Comparative sequence analysis of a gene-rich cluster at human chromosome 12p13 and its syntenic region in mouse chromosome 6. Genome Res. 8: 29-40.
5. Chissoe, S.L., M.A. Marra, L. Hillier, R. Brinkman, R.K. Wilson, and R.H. Waterston. 1997. Representation of cloned genomic sequences in two sequencing vectors: Correlation of DNA sequence and subclone distribution. Nucleic Acids Res. 25: 2960-2966.
6. Clark, A.G. and T.S. Whittam. 1992. Sequencing errors and molecular evolutionary analysis. Mol. Biol. Evol. 9: 744-752.
7. Claverie, J.M. 1994. A streamlined random sequencing strategy for finding coding exons. Genomics 23: 575-581.
8. Edwards, A. and C.T. Caskey. 1990. Closure strategies for random DNA sequencing. Methods: Companion Methods Enzymol. 1: 41-47.
9. Ewing, B. and P. Green. 1998. Base-calling of automated sequencer traces using phred. II. Error probabilities. Genome Res. 8: 186-194.
10. Ewing, B., L. Hillier, M.C. Wendl, and P. Green. 1998. Base-calling of automated sequencer traces using phred. 1. Accuracy assessment. Genome Res. 8: 175-185.
11. Favello, A., L. Hillier, and R.K. Wilson. 1995. Genomic DNA sequencing methods. Methods Cell Biol. 48: 551-569.
12. Florea, L., G. Hartzell, Z. Zhang, G.M. Rubin, and W. Miller. 1998. A computer program for aligning a cDNA sequence with a genomic DNA sequence. Genome Res. 8: 967-974.
13. Goodman, L. 1998. Random shotgun fire. Genome Res. 8: 567-568.
14. Green, P. 1997. Against a whole-genome shotgun. Genome Res. 7: 410-417.
15. Hardison, R.C., J. Oeltjen, and W. Miller. 1997. Long human-mouse sequence alignments reveal novel regulatory elements: A reason to sequence the mouse genome. Genome Res. 7: 959-966.
16. Kamb, A., C. Wang, A. Thomas, B.S. DeHoff, F.H. Norris, K. Richardson, J. Rine, M.H. Skolnick, and P.R.J. Rosteck. 1995. Software trapping: A strategy for finding genes in large genomic regions. Comp. Biomed. Res. 28: 140-153.
17. Lander, E.S. and M.S. Waterman. 1988. Genomic mapping by fingerprinting random clones: A mathematical analysis. Genomics 2: 231-239.
18. Lee, L.G., C.R. Connell, S.L. Woo, R.D. Cheng, B.F. McArdle, C.W. Fuller, N.D. Halloran, and R.K. Wilson. 1992. DNA sequencing with dye-labeled terminators and T7 DNA polymerase: Effect of dyes and dNTPs on incorporation of dye-terminators and probability analysis of termination fragments. Nucleic Acids Res. 20: 2471-2483.
19. Marshall, E. 1995. Human genome project. Emphasis turns from mapping to large-scale sequencing. Science 268: 1270-1271.
20. Olson, M. and P. Green. 1998. A "quality-first" credo for the Human Genome Project. Genome Res. 8: 414-415.
21. Roach, J.C., C. Boysen, K. Wang, and L. Hood. 1995. Pairwise end sequencing: A unified approach to genomic mapping and sequencing. Genomics 26: 345-353.
22. Smith, G.D. and K.E. Bernstein. 1995. BULLET: A computer simulation of shotgun DNA sequencing. Comp. Appl. Biosci. 11: 155-157.
23. 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.
24. Weber, J.L. and E.W. Myers. 1997. Human whole-genome shotgun sequencing. Genome Res. 7: 401-409.