ProtoMap: automatic classification of protein sequences and hierarchy of protein families

The ProtoMap site offers an exhaustive classification of all proteins in th e SWISS-PROT database, into groups of related proteins. The classification is based on analysis of all pairwise similarities among protein sequences, The analysis makes essential use of transitivity to identify homologies amo ng proteins. Within each group of the classification, every two members are either directly or transitively related. However, transitivity is applied restrictively in order to prevent unrelated proteins from clustering togeth er, The classification is done at different levels of confidence, and yield s a hierarchical organization of all:proteins. The resulting classification splits the protein space into well-defined groups of proteins, which are c losely correlated with natural biological families and superfamilies. Many clusters contain protein sequences that are not classified by other databas es. The hierarchical organization suggested by our analysis may help in det ecting finer subfamilies in families of known proteins. In addition it brin gs forth interesting relationships between protein families, upon which loc al maps for the neighborhood of protein families can be sketched. The Proto Map web server can be accessed at http://www.protomap.cs.huji.ac.il.