PFDB - A PROTEIN FAMILIES DATABASE FOR MACINTOSH COMPUTERS - THE EFFECTIVENESS OF ITS ORGANIZATION IN SEARCHING FOR PROTEIN SIMILARITY

A protein sequence database (PFDB) containing about 11,000 entries is available for Macintosh computers. The PFDB can be easily updated by i mporting sequences from the PIR collection through the internet. The m ost important feature of the database is its organization in families of closely related sequences, each family being characterized by its a verage dipeptide composition [Petrilli (1993), Comput. Appl. Biosci. 2 , 89-93]. This allows one to perform a rapid and sensitive protein sim ilarity search by comparing the precalculated family dipeptide composi tion with that of the query sequence by a linear correlation coefficie nt. An example of an application in which a new protein was classified by using a sequence of a fragment just 19 residues long is reported.