Network release of the protein family pattern bank PROF_PAT 1.1

Using an automated technique, we compiled a new network release of the prot ein family pattern bank composed of 7083 groups of related proteins coverin g 52,000 amino acid sequences from SWISS-PROT release 34 and TREMBL release 1. The tool for quick search for local similarity between a query amino ac id sequence and SWISS-PROT proteins has been developed, which may help with primary identification of novel sequences function. The sensitivity and se lectivity of the method were evaluated by comparing the patterns with all p roteins of the parent bank and a number of proteins from its recent release . The patterns have ''positive" or "conditional-positive" similarity to mor e than 55,000 proteins of the parent bank. The bank of patterns is suppleme nted by flexible fast search programs. Both the local and network versions make it possible to select a similarity matrix (PAM, BLOSUM, etc.) and spec ify the level of similarity (from exact match to low similarity).