Affiliations: Theoretical Department, Research Institute of
Molecular Biology, SRC VB "Vector", Koltsovo,
Novosibirsk region, 630559, Russia. Tel.: +7 3832 36 64 79; Fax: +7 3832 36 74
09; E-mail: [email protected] | Laboratory of Theoretical Genetics, Institute of
Cytology and Genetics, Lavrentyev Ave., 10, Novosibirsk, 630090, Russia. Tel.:
+7 3832 33 31 19; Fax: +7 3832 33 12 78; E-mail: [email protected]
Note: [] Corresponding author
Abstract: 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
for 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.
Keywords: protein families, patterns, motifs, similarity search, data banks, amino acid sequences, protein comparison
