Database of patterns PROF_PAT for detecting local similarities

We have developed PROF_PAT, a database of patterns, constructed for groups of related proteins and designed to maximize representation of amino acid sequences from the SWISS-PROT database. The purpose of the current study was to demonstrate that PROT_PAT is not only as good as known analogs but surpasses them in some features. 10938 new amino acid sequences from the SWISS-PROT bank were compared with patterns constructed for protein families in the PROF_PAT 1.10 bank. The aim of the comparisons was to estimate some threshold values of "Score" parameter to distinguish random similarities from significant ones. From the 10938 new sequences, 638 did not reveal any similarities with PROF_PAT patterns. Cases of found similarities were divided into three sets: 'positive', 'putative' (or 'unknown'), and 'false positive', containing 7719, 2297 and 284 sequences respectively. Using 20 amino acid sequences from the TrEMBL bank that have no descriptions, PROF_PAT demonstrated specificity at a level that was as good as the best-known "secondary" banks. At the same time, its pattern content and variety of included proteins was significantly richer, and its search speed was 3-10 times higher than those of any other protein family bank used for comparison.