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Bioinformatics Vol. 17 no. 4 2001
Pages 343-348
© 2001 Oxford University Press

Original Paper

NIFAS: visual analysis of domain evolution in proteins

Christian E. V. Storm and Erik L. L. Sonnhammer

Center for Genomics Research, Karolinska Institutet, 171 77 Stockholm, Sweden

Received on October 11, 2000 ; revised on December 8, 2000 ; accepted on December 13, 2000

Motivation: Multi-domain proteins have evolved by insertions or deletions of distinct protein domains. Tracing the history of a certain domain combination can be important for functional annotation of multi-domain proteins, and for understanding the function of individual domains. In order to analyze the evolutionary history of the domains in modular proteins it is desirable to inspect a phylogenetic tree based on sequence divergence with the modular architecture of the sequences superimposed on the tree.

Result: A Java applet, NIFAS, that integrates graphical domain schematics for each sequence in an evolutionary tree was developed. NIFAS retrieves domain information from the Pfam database and uses CLUSTAL W to calculate a tree for a given Pfam domain. The tree can be displayed with symbolic bootstrap values, and to allow the user to focus on a part of the tree, the layout can be altered by swapping nodes, changing the outgroup, and showing/collapsing subtrees. NIFAS is integrated with the Pfam database and is accessible over the internet (http://www.cgr.ki.se/Pfam). As an example, we use NIFAS to analyze the evolution of domains in Protein Kinases C.

Contact: christian.storm{at}cgr.ki.se


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