A RAPID algorithm for sequence database comparisons: Application to the identification of vector contamination in the EMBL databases

Bioinformatics

Volumn 15, Issue 2, 1999, Pages 111-121

  Miller, C ^a,b   Gurd, J ^b   Brass, A ^a  

^a UNIVERSITY OF MANCHESTER   (United Kingdom)

^b UNIVERSITY OF MANCHESTER   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHM; ARTICLE; CLONING VECTOR; COMPUTER PROGRAM; CONTAMINATION; DATA BASE; DNA SEQUENCE; PRIORITY JOURNAL; RECEIVER OPERATING CHARACTERISTIC;

EID: 0033049747     PISSN: 13674803     EISSN: 13674811     Source Type: Journal    
DOI: 10.1093/bioinformatics/15.2.111     Document Type: Article

References (17)

1. Altschul, S., Gish W., Miller, W., Myers, E.W. and Lipman, D.J. (1990) Basic Local Alignment Tool. J. Mol. Biol., 215, 403-410.
2. Atteson, K. (1998) Calculating the exact probability of language like patterns in biomoleculur sequences ISMB-98, pp. 14-17. AAAI Press, California.
3. Bishop, M. and Thompson, E. (1984) Fast computer search tor similar DNA sequences. Nucleic Acids Res., 12, 5471-5474.
4. Boguski, M.S. and Schuler, G.D. (1995) Establishing a Human Transcript Map. Nature Genetics, 10,369-371.
5. Gibbs, A.J. and McIntyre, G.A. (1970) The diagram, a method for comparing sequences Eur. J. Biochem., 16, 1-11.
6. Harger, C. et al. (1998) The Genome Sequence DataBase (GSDB): improving data quality and data access. Nucleic Acids Res., 26, 21-26.
7. Hough, P.V.C. (1962) Methods and Means for Recognizing Complex Patterns. US Patent 3,069,654.
8. Lamperti, E.D., Kittelberger, J.M., Smith, T.F. and Villa-Komaroff, L. (1992) Corruption of genomic databases with anomalous sequence. Nucleic Acids Res., 20, 2741-2747.
9. Lanfranchi, G. et al. (1996) Identification of 4370 expressed sequence tags from a 3-end-specific cDNA library of human skeletal muscle by DNA sequencing and filter hybridization. Genome Res., 6, 35-42.
10. Parsons, J.D. (1995) Miropeats: graphical DNA sequence comparisons. Comput. Applic. Biosci., 11, 615-619.
11. Pearson, W. (1990) Rapid and sensitive sequence comparison with FASTP and FASTA. Methods Enzymol., 183, 63-98.
12. Rigoutsos, I. and Califano, A. (1994) Searching in Parallel for similar strings IEEE Comp. Sci. Eng., Summer, 60-75.
13. Shah, I. and Hunter, L. (1997) Proceedings of the Fifth International Conference on Intelligent Systems for Molecular Biology. AAAI Press, California, pp. 276-283.
14. Shannon, C.E. (1948) A mathematical theory of communication. Bell Syst. Tech. J., 27, 379-423 and 623-656, July and October.
15. Smith, T.F. and Waterman, M.S. (1981) Identification of common molecular subsequences. J. Mol. Biol., 147, 195-197.
16. Swets, J. (1982) Measuring the Accuracy of Diagnostic Systems. Academic Press, New York.
17. Wilbur, W.J. and Lipman, D.J. (1983) Rapid similarity searches of nucleic acid and protein data banks Proc. Natl Acad. Sci. USA, 80, 726-730.