title: NIFAS: visual analysis of domain evolution in proteins.
abstract: 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.
authors: Center for Genomics Research, Karolinska Institutet, 171 77 Stockholm, Sweden.
authors: C E
authors: CE
authors: Storm
authors: E L
authors: EL
authors: Sonnhammer
mesh_terms: 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
chemical_list: D011506:Proteins; D011493:Protein Kinase C