Functional classification of proteins using a nearest neighbour algorithm

In Silico Biology

Volumn 3, Issue 3, 2003, Pages 265-275

  Keck, Hans Peter ^a   Wetter, Thomas ^b  

^a Axaron Bioscience AG   (Germany)

^b UNIVERSITY HOSPITAL HEIDELBERG   (Germany)

Author keywords

Classification; Genome analysis; Machine learning; Nearest neighbor algorithm; Protein function

Indexed keywords

PROTEIN;

ACCURACY; ALGORITHM; AMINO ACID SEQUENCE; ARTICLE; AUTOMATION; CLASSIFICATION; COMPUTER ANALYSIS; COMPUTER PROGRAM; COMPUTER SYSTEM; CONTROLLED STUDY; DATA ANALYSIS; ESCHERICHIA COLI; GENOME; MOUSE; NONHUMAN; PREDICTION; PROTEIN FUNCTION; QUALITY CONTROL; SENSITIVITY AND SPECIFICITY; SEQUENCE ANALYSIS; SEQUENCE HOMOLOGY; STAFF TRAINING; SWISS-PROT; YEAST;

ALGORITHMS; DATABASES, PROTEIN; PROGRAMMING LANGUAGES; PROTEINS; SEQUENCE ANALYSIS, PROTEIN; SOFTWARE DESIGN;

EID: 0344740820     PISSN: 13866338     EISSN: None     Source Type: Journal    
DOI: None     Document Type: Article

References (16)

1. Aha, D. W., Kibler, D. and Albert, M. K. (1991). Instance-based learning algorithms. Machine Learning 6, 37-66.
2. Altschul, S. F., Madden, T. L., Schaffer, A. A., Zhang, J., Zhang, Z., Miller, W. and Lipman, D. J. (1997). Gapped BLAST and PSI-BLAST: A new generation of protein database search programs. Nucleic Acids Res. 25, 3389-3402.
3. Cost, S. and Salzberg, S. (1993). A weighted nearest neighbor algorithm for learning with symbolic features. Machine Learning 10, 57-78.
4. Cover, T. and Hart, P. (1967). Nearest neighbor pattern classification. IEEE Transactions on Information Theory 13, 21-27.
5. Dasarathy, B. V. (1991). Nearest Neighbor (NN) Norms: NN Pattern Classification Techniques. IEEE Computer Society Press.
6. The Expressed Gene Anatomy Database (EGAD).
7. Eisenhaber, F. and Bork, P. (1999). Evaluation of human-readable annotation in biomolecular sequence databases with biological rule libraries. Bioinformatics 15, 528-535.
8. Etzold, T., Ulyanov, A. and Argos, P. (1996). SRS: Information retrieval system for molecular biology data banks. Methods Enzymol. 266, 114-128.
9. GenProtEC: E. Coli Genome and Proteome Database.
10. Gene ontology consortium home page.
11. Mips - Saccharomyces Cerevisiae - The Yeast Genome.
12. Nakai, K. and Kanehisa, M. (1991). Expert system for predicting protein localization sites in gram-negative bacteria. Proteins 11, 95-110.
13. Nakai, K. and Kanehisa, M. (1992). A knowledge base for predicting protein localization sites in eukaryotic cells. Genomics 14, 897-911.
14. The online medical dictionary.
15. Rachlin, J., Kasif, S., Salzberg, S. and Aha, D. W. (1994). Towards a better understanding of memory-based and bayesian classifiers. Proceedings of the Eleventh International Machine Learning Conference.
16. Tamames, J., Ouzounis, C., Casari, G., Sander, C. and Valencia, A. (1998). EUCLID: Automatic classification of proteins in functional classes by their database annotations. Bioinformatics 14, 542-543.