Definition of the tempo of sequence diversity across an alignment and automatic identification of sequence motifs: Application to protein homologous families and superfamilies

Protein Science

Volumn 11, Issue 12, 2002, Pages 2825-2835

  May, Alex C W ^a  

^a NATIONAL INSTITUTE FOR MEDICAL RESEARCH   (United Kingdom)

Author keywords

Multiple sequence alignment; Optimal segmentation; Protein homologous family; Protein superfamily; Sequence motif

Indexed keywords

AMINO ACID SEQUENCE; ARTICLE; AUTOANALYSIS; PRIORITY JOURNAL; PROTEIN FAMILY; PROTEIN FOLDING; PROTEIN MOTIF; PROTEIN STRUCTURE; SEQUENCE ALIGNMENT; STRUCTURE ANALYSIS; TECHNIQUE; BIOLOGY; CHEMISTRY; CLASSIFICATION; GENETICS; NUCLEOTIDE SEQUENCE; PROTEIN DATABASE; SEQUENCE HOMOLOGY;

PROTEIN;

AMINO ACID MOTIFS; COMPUTATIONAL BIOLOGY; CONSERVED SEQUENCE; DATABASES, PROTEIN; PROTEINS; SEQUENCE ALIGNMENT; SEQUENCE HOMOLOGY, AMINO ACID;

EID: 0036892555     PISSN: 09618368     EISSN: None     Source Type: Journal    
DOI: 10.1110/ps.0211202     Document Type: Article

References (29)

1. Andre, C., Vincens, P., Boisvieux, J.F., and Hazout, S. 2001. MOSAIC: Segmenting multiple aligned DNA sequences. Bioinformatics 17: 196-197.
2. Anfinsen, C.B. 1973. Principles that govern the folding of protein chains. Science 181: 223-230.
3. Axe, D.D. 2000. Extreme functional sensitivity to conservative amino acid changes on enzyme exteriors. J. Mol. Biol. 301: 585-595.
4. Bement, T.R. and Waterman, M.S. 1977. Locating maximum variance segments in sequential data. Math. Geol. 9: 55-61.
5. Blundell, T.L., Sibanda, B.L., Sternberg, M.J.E., and Thornton, J.M. 1987. Knowledge-based prediction of protein structures and the design of novel molecules. Nature 326: 347-352.
6. Chothia, C. and Lesk, A.M. 1986. The relation between the divergence of sequence and structure in proteins. EMBO J. 5: 823-826.
7. Doolittle, R.F. 1986. Of Urfs and Orfs: A Primer on How to Analyze Derived Amino Acid Sequences. University Science Books, Mill Valley, CA.
8. Durbin, R., Eddy, S.R., Krogh, A., and Mitchison, G. 1998. Biological Sequence Analysis: Probalistic Models of Proteins and Nucleic Acids. Cambridge University Press, Cambridge, MA.
9. Everitt, B. 1993. Cluster Analysis. E. Arnold, London.
10. Gordon, A.D. 1996. A survey of constrained classification. Comput. Stat. Data Anal. 21: 17-29.
11. Hawkins, D.M. and Merriam, D.F. 1973. Optimal zonation of digitized sequential data. Math. Geol. 5: 389-395.
12. Henikoff, S. and Henikoff, J.G. 1994. Position-based sequence weights. J. Mol. Biol. 243: 574-578.
13. Herrmann, G., Schon, A., Brack-Werner, R., and Werner, T. 1996. CONRAD: A method for identification of variable and conserved regions within proteins by scale-space filtering. Comput. Appl. Biosci. 12: 197-203.
14. Heymann, J.B. and Engel, A. 2000. Structural clues in the sequences of the aquaporins. J. Mol. Biol. 295: 1039-1053.
15. Hofmann, K., Bucher, P., Falquet, L., and Bairoch, A. 1999. The PROSITE database, its status in 1999. Nucleic Acids Res. 27: 215-219.
16. Johnson, M.S., May, A.C.W., Rodionov, M.A., and Overington, J.P. 1996. Discrimination of common protein folds: Application of protein structure to sequence/structure comparisons. Methods Enzymol. 266: 575-598.
17. Jonassen, I., Eidhammer, I., and Taylor, W.R. 1999. Discovery of local packing motifs in protein structures. Proteins 34: 206-219.
18. Lanyon, S.M. 1985. Detecting internal inconsistencies in distance data. Syst. Zool. 34: 397-403.
19. May, A.C.W. 1996. Pairwise iterative superposition of distantly related proteins and assessment of the significance of 3-D structural similarity. Protein Eng. 9: 1093-1101.
20. -. 1999a. A cautionary note on interpretation of hierarchical classifications of protein folds. Struct. Fold. Des. 7: R213.
21. -. 1999b. Toward more meaningful hierarchical classification of protein three-dimensional structures. Proteins 37: 20-29.
22. -. 2001. Optimal classification of protein sequences and selection of representative sets from multiple alignments: Application to homologous families and lessons for structural genomics. Protein Eng. 14: 209-217.
23. Mizuguchi, K., Deane, C.M., Blundell, T.L., and Overington, J.P. 1998. HOMSTRAD: A database of protein structure alignments for homologous families. Protein Sci. 7: 2469-2471.
24. Murzin, A.G., Brenner, S.E., Hubbard, T., and Chothia, C. 1995. SCOP: A structural classification of proteins database for the investigation of sequences and structures. J. Mol. Biol. 247: 536-540.
25. Romesburg, H.C. 1984. Cluster Analysis for Researchers. Lifetime Learning Publications, Belmont, CA.
26. Shenkin, P.S., Erman, B., and Mastrandrea, L.D. 1991. Information-theoretical entropy as a measure of sequence variability. Proteins 11: 297-313.
27. Smith, T.F. 1999. The art of matchmaking: Sequence alignment methods and their structural implications. Struct. Fold. Des. 7: R7-R12.
28. Sowdhamini, R., Burke, D.F., Huang, J.F., Mizuguchi, K., Nagarajaram, H.A., Srinivasan, N., Steward, R.E., and Blundell, T.L. 1998. CAMPASS: A database of structurally aligned protein superfamilies. Structure 6: 1087-1094.
29. Stojanovic, N., Florea, L., Riemer, C., Gumucio, D., Slightom, J., Goodman, M., Miller, W., and Hardison, R. 1999. Comparison of five methods for finding conserved sequences in multiple alignments of gene regulatory regions. Nucleic Acids Res. 27: 3899-3910.