Kohonen map as a visualization tool for the analysis of protein sequences: Multiple alignments, domains and segments of secondary structures

Bioinformatics

Volumn 12, Issue 6, 1996, Pages 447-454

  Hanke, Jens ^a   Reich, Jens G ^a  

^a Department of Bwinfor matics ^*  (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACID SEQUENCE; ARTICLE; ARTIFICIAL NEURAL NETWORK; CLUSTER ANALYSIS; COMPUTER PROGRAM; PRIORITY JOURNAL; PROTEIN FAMILY; PROTEIN SECONDARY STRUCTURE;

AMINO ACID SEQUENCE; COMPUTERS; DATABASES, FACTUAL; MOLECULAR SEQUENCE DATA; MOLECULAR STRUCTURE; NEURAL NETWORKS (COMPUTER); PROTEIN STRUCTURE, SECONDARY; PROTEINS; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS; SEQUENCE HOMOLOGY, AMINO ACID; SOFTWARE;

EID: 0030449297     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/12.6.447     Document Type: Article

References (16)

1. Altschul.S., Gish.W., Miller.W., Mycrs.E.W. and Lipman, D.J. (1990) Basic local alignment search tool. J. Mol. Biol, 215, 403-410.
2. Bernstein, F.C, Koetzle, T.F., Wilhams, G.J.B., Meyer, E.F., Brice, M.D., Rodgers, J.R.. Kennard, O., Shimanouchi, T. and Tasumi, M. (1977) The Protein Data Bank: a computer-based archival file for macro-molecular structures. J. Mol. Biol., 112, 535-542.
3. Caspers.G.J, Leunissen, J.A. and De-Jong, W.W. (1995) The expanding smal heat-shock protein family, and structure predictions of the conserved 'alpha-crystallin domainT. J. Mol. Evol., 40, 238-248.
4. Dayhof, T. M. O., Schwartz, R.M. and Oreutt, B.C. (1978) A model of evolutionary change in proteins. In Dayhoff.M.O. (ed.), Alias of Protein Sequence and Structure. National Biomedical Research Foundation, Washington, DC, Vol. V, Suppl. 3, pp. 345-352.
5. Ferran.E.A and Ferrara, P. (1991) Topological maps of protein sequences. Bwl. Cvbern., 65, 451-458.
6. Gribskov, M., Lthy, R and Eisenberg, D. (1990) Profile analysis. Methods Enzymol., 183, 146-159.
7. Hanke.J., Beckmann, G., Bork, P. and Reich.J.G. (1996) Self organizing hierarchic networks for pattern recognition in protein sequence. Protein Sci., 5, 72-84.
8. Henikoff, S. and HenikoffJ.G. (1991) Automated assembly of protein blocks for data base searching. Nucleic Acids Res., 19, 6565-6572.
9. Henikoff, S. and Henikoff, J.G. (1992) Amino acid substitution matrices from protein blocks. Proc. Nail Acad. Sci. USA, 89, 10915-10919.
10. Holm.L. and Sander.C. (1994) The FSSP database of structurally aligned protein fold families. Nucleic Acids Res., 22, 3600-3609.
11. JefTrey.H.J. (1990) Chaos game representation of gene structure. Nucleic Acids Res., 18, 2163-2170.
12. Kabsch, W. and Sander, C. (1983) How good are predictions of protein secondary structure? FEBS Lett., 155, 179-182.
13. Kohonen, T. (1989) Self-Organization and Associative Memory. Springer Verlag, Berlin.
14. Lynch, Th.J. (1985) Data Compression Techniques and Applications. Lifetime Learning Publications, Belmont.
15. Swayne, D.F., Cook.B.D. and Buja.A. (1991) User's Manual for XGobi a Dynamic Program of Data Analysis Implemented in the X Window System. Bellcore Technical Memorandum.
16. Taylor, W.R. (1986) Identification of protein sequence homology by consensus template alignment. J. Mol. Biol., 188, 233-258.