NIFAS: visual analysis of domain evolution in proteins.
BACKGROUND
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.


RESULTS
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.
Storm
C E
CE
Center for Genomics Research, Karolinska Institutet, 171 77 Stockholm, Sweden.
Sonnhammer
E L
EL
D003196:Computer Graphics; D019143:Evolution, Molecular; D006801:Humans; D007091:Image Processing, Computer-Assisted; D011493:Protein Kinase C / Q000737:chemistry* / Q000145:classification; D017434:Protein Structure, Tertiary; D011506:Proteins / Q000737:chemistry* / Q000145:classification; D012984:Software
D011506:Proteins; D011493:Protein Kinase C