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

The method of Kohonen maps, a special form of neural networks, was applied as a visualization tool for the analysis of protein sequence similarity. The procedure converts sequence (domains, aligned sequences, segments of secondary structure) into a characteristic signal matrix. This conversion depends on the property or replacement score vector selected by the user. Similar sequences have small distance in the signal space. The trained Kohonen network is functionally equivalent to an unsupervised non-linear cluster analyzer. Protein families, or aligned sequences, or segments of similar secondary structure, aggregate as clusters, and their proximity may be inspected on a color screen or on paper. Pull-down menus permit access to background information in the established text-oriented way.

[1]  C. Sander,et al.  The FSSP database of structurally aligned protein fold families. , 1994, Nucleic acids research.

[2]  S. Henikoff,et al.  Automated assembly of protein blocks for database searching. , 1991, Nucleic acids research.

[3]  Teuvo Kohonen,et al.  Self-Organization and Associative Memory , 1988 .

[4]  W. Taylor,et al.  Identification of protein sequence homology by consensus template alignment. , 1986, Journal of molecular biology.

[5]  W. Kabsch,et al.  How good are predictions of protein secondary structure? , 1983, FEBS letters.

[6]  Peer Bork,et al.  Self‐organizing hierarchic networks for pattern recognition in protein sequence , 1996, Protein science : a publication of the Protein Society.

[7]  S. Henikoff,et al.  Amino acid substitution matrices from protein blocks. , 1992, Proceedings of the National Academy of Sciences of the United States of America.

[8]  M. Gribskov,et al.  [9] Profile analysis , 1990 .

[9]  Thomas J. Lynch,et al.  Data compression techniques and applications , 1985 .

[10]  G J Williams,et al.  The Protein Data Bank: a computer-based archival file for macromolecular structures. , 1977, Journal of molecular biology.

[11]  H. J. Jeffrey.  Chaos game representation of gene structure. , 1990, Nucleic acids research.

[12]  E. Myers,et al.  Basic local alignment search tool. , 1990, Journal of molecular biology.