Comparative accuracy of methods for protein sequence similarity search

Bioinformatics

Volumn 14, Issue 1, 1998, Pages 40-47

  Agarwal, Pankaj ^a,b   States, David J ^a  

^a WASHINGTON UNIVERSITY SCHOOL OF MEDICINE   (United States)

^b GLAXOSMITHKLINE   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

ACCURACY; AMINO ACID SEQUENCE; ARTICLE; BIOSTATISTICS; COMPARATIVE STUDY; COMPUTER PROGRAM; DATA BASE; PRIORITY JOURNAL; RECEIVER OPERATING CHARACTERISTIC; SEQUENCE HOMOLOGY;

EID: 0031827544     PISSN: 13674803     EISSN: 13674811     Source Type: Journal    
DOI: 10.1093/bioinformatics/14.1.40     Document Type: Article

References (20)

1. Agarwal, P. and States, D. (1996) A Bayesian evolutionary distance for parametricaily aligned sequences. J. Comput. Biol., 3, 1-17.
2. Altschul, S. (1993) A protein alignment scoring system sensitive at all evolutionary distances. J. Mol. Evol., 36, 290-300.
3. Altschul, S. and Gish, W (1996) Local alignment statistics. Methods Enzymol., 266, 460-480.
4. Altschul, S., Gish, W., Miller, W., Myers, E. and Lipman, D. (1990) Basic local alignment search tool. J. Mol. Biol., 215, 403-410.
5. Altschul, S., Boguski, M., Gish, W. and Wootton, J. (1994) Issues in searching molecular sequence databases. Nature Genet., 6, 119-129.
6. Argos, P., Vingron, M. and Vogt, G. (1991) Protein sequence comparisons: methods and significance. Protein Eng., 4, 375-383.
7. Barker, W., George, D. and Hunt, L (1990) Protein sequence database. Methods Enzymol., 183, 31-49.
8. Bishop, M. and Thompson, E. (1986) Maximum likelihood alignment of DNA sequences. J. Mol. Biol., 190, 159-165.
9. Bucher, P. and Hoffman, K. (1996) A sequence similarity algorithm based on a probabilistic interpretation of an alignment scoring system. In States, D., Agarwal, P., Gaasterland, T., Hunter, L. and Smith, R. (eds), ISMB-4 AAAI Press, Menlo Park, CA.
10. Duda, R. and Hart, P. (1973) Pattern Classification and Scene Analysis. John Wiley and Sons.
11. Eddy, S. (1996) Hidden Markov models. Curr Opin. Struct. Biol., 6, 361-365.
12. Eddy, S., Mitchison, G. and Durbin, R. (1995) Maximum discrimination hidden Markov models of sequence consensus. J. Comput Biol., 2, 9-23.
13. Gribskov, M. and Robinson, N. (1996) The use of receiver operating characteristic (ROC) analysis to evaluate sequence matching. Comput. Chem., 20, 25-34.
14. Krogh, A., Brown, M., Mian, I., Sjölander, K. and Haussler, D. (1994) Hidden Markov models in computational biology: Applications to protein modeling. J. Mol. Biol., 235, 1501-1531.
15. Needleman, S. and Wunsch, C. (1970) A general method applicable to the search for similarities in the amino acid sequences of two proteins. J. Mol. Biol., 48, 444-453.
16. Pearson, W. (1995) Comparison of methods for searching protein sequence databases. Protein Sci., 4, 1145-1160.
17. Pearson, W. and Lipman, D. (1988) Improved tools for biological sequence comparison. Proc. Natl Acad. Sci. USA, 85, 2444-2448.
18. Saqi, M. and Sternberg, M. (1991) A simple method to generate non-trivial alternate alignments of protein sequences. J. Mol. Biol., 219, 727-732.
19. Smith, T. and Waterman, M. (1981) Identification of common molecular subsequences. J. Mol. Biol., 147, 195-197.
20. Zuker, M. (1991) Suboptimal sequence alignment in molecular biology: Alignment with error analysis. J. Mol. Biol., 221, 403-420.