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Bioinformatics Vol. 16 no. 4 2000
Pages 358-366
© 2000 Oxford University Press

PROF_ PAT 1.3: Updated database of patterns used to detect local similarities

A. G. Bachinsky 1,*, A. S. Frolov 2, A. N. Naumochkin 1, L. Ph. Nizolenko 1 and A. A. Yarigin 1

1 Theoretical Department, Research Institute of Molecular Biology, SRC VB ‘Vector’,Koltsovo, Novosibirsk region, 630559, Russia
2 Institute of Cytology and Genetics SB RAS, Novosibirsk, 630090, Russia

Received on June 2, 1999 ; revised on September 29, 1999 ; accepted on October 20, 1999

*To whom correspondence should be addressed.

Motivation: When analysing novel protein sequences, it is now essential to extend search strategies to include a range of ‘secondary’ databases. Pattern databases have become vital tools for identifying distant relationships in sequences, and hence for predicting protein function and structure. The main drawback of such methods is the relatively small representation of proteins in trial samples at the time of their construction. Therefore, a negative result of an amino acid sequence comparison with such a databank forces a researcher to search for similarities in the original protein banks. We developed a database of patterns constructed for groups of related proteins with maximum representation of amino acid sequences of SWISS-PROT in the groups.

Results: Software tools and a new method have been designed to construct patterns of protein families. By using such method, a new version of databank of protein family patterns, PROF_ PAT 1.3, is produced. This bank is based on SWISS-PROT (r1.38) and TrEMBL (r1.11), and contains patterns of more than 13 000 groups of related proteins in a format similar to that of the PROSITE. Motifs of patterns, which had the minimum level of probability to be found in random sequences, were selected. Flexible fast search program accompanies the bank. The researcher can specify a similarity matrix (the type PAM, BLOSUM and other). Variable levels of similarity can be set (permitting search strategies ranging from exact matches to increasing levels of ‘fuzziness’).

Availability: The Internet address for comparing sequences with the bank is: http://wwwmgs.bionet.nsc.ru/mgs/programs/prof_pat/. The local version of the bank and search programs (approximately 50 Mb) is available via ftp: ftp://ftp.bionet.nsc.ru/pub/biology/vector/prof_pat/, and ftp://ftp.ebi.ac.uk/pub/databases/prof_pat/. Another appropriate way for its external use is to mail amino acid sequences to bachin@vector.nsc.ru for comparison with PROF_ PAT 1.3.

Contact: bachin{at}vector.nsc.ru


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