SITECON: a tool for detecting conservative conformational and physicochemical properties in transcription factor binding site alignments and for site recognition.

The local DNA conformation in the region of transcription factor binding sites, determined by context, is one of the factors underlying the specificity of DNA-protein interactions. Analysis of the local conformation of a set of functional DNA sequences may allow for determination of the conservative conformational and physicochemical parameters reflecting molecular mechanisms of interaction. The web resource SITECON is designed to detect conservative conformational and physicochemical properties in transcription factor binding sites, contains a knowledge base of conservative properties for >100 high-quality sample sites and allows for recognition of potential transcription factor binding sites based on conservative properties from both the knowledge base and the results of analysis of a sample proposed by a user. The resource SITECON is available at http://wwwmgs.bionet.nsc.ru/mgs/programs/sitecon/.

[Bank of samples from the Prof_Pat protein family, assessment of efficacy]. / Bank obrazov belkovykh semeistv PROF_PAT, otsenka éffektivnosti.

The PROF_PAT protein pattern database has been created and maintained so as to comprise the maximal number of the SWISS-PROT + TrEMBL proteins as patterns. The present paper describes some characteristic features of PROF_PAT to assist the potential user. New amino acid sequences (10938) from the SWISS-PROT database have been analyzed to determine the boundary values of the "score" parameter to distinguish random and significant similarities. Analysis through the Internet of 20 amino acid sequences having no descriptions in the TrEMBL database demonstrated that PROF_PAT, being highly competitive with its counterparts in specificity, surpasses them in amplitude and variety of proteins, working several times as fast. The real representation of protein families in the PROF_PAT database (release 1.11), which contains 50,149 patterns of 344,429 proteins, has been estimated at 31,450.

[mRNA-FAST (mRNA-Function, Activity, STructure) computer system]. / Komp'iuternaia sistema mRNA-FAST (mRNA-Function, Activity, Structure).

Computer system mRNA-FAST (mRNA--Function, Activity, STructure; http://wwwmgs.bionet.nsc.ru/mgs/dbases/trsig/) is described. The system has been developed to analyze nucleotide sequences of mRNA and to measure their essential properties. The system compiles the data base on translation signals including nucleotide sequences of the regulatory regions with structural and experimental information on their specific activities. It also contains programs to search for local homology between mRNA and translation signals, to search for potential signals basing on analysis of the oligonucleotide dictionaries, and to model secondary RNA structure. Possible applications of the system mRNA-FAST are discussed.

[Properties of artificial evolution of proteins and peptides]. / Issledovanie svoistv iskusstvenno évoliutsii belkov i peptidov.

In vitro evolution is used to study protein sequences, structures, and interactions and to obtain proteins with new properties. To analyze the specific features of this process in experiments with phage display, we studied the amino acid composition of selected sequences, constructed a matrix of amino acid substitutions, and identified pairs of coadaptive substitutions. Amino acid frequency proved to be tightly associated with the number of corresponding codons; numerous correlated substitutions were found.

[Regulation of eukaryotic gene transcription: description in the TRRD database]. / Reguliatsiia transkriptsii genov éukariot: opisanie v baze dannykh TRDD.

The structure of the Transcription Regulatory Regions Database (TRRD) and the principles of considering transcription regulation of eukaryotic genes in TRRD are concerned. Formal description of the structural and functional organization of the regulatory gene regions is illustrated with examples. By now, TRRD is based on 3500 original works and contains data on transcription regulation of more than 1100 genes known to possess more than 5000 transcription factor-binding sites and about 1600 regulatory elements (promoters, enhancers, silencers). TRRD is available at http://www.bionet.nsc.ru/trrd/.

Integrated databases and computer systems for studying eukaryotic gene expression.

MOTIVATION: The goal of the work was to develop a WWW-oriented computer system providing a maximal integration of informational and software resources on the regulation of gene expression and navigation through them. Rapid growth of the variety and volume of information accumulated in the databases on regulation of gene expression necessarily requires the development of computer systems for automated discovery of the knowledge that can be further used for analysis of regulatory genomic sequences. RESULTS: The GeneExpress system developed includes the following major informational and software modules: (1) Transcription Regulation (TRRD) module, which contains the databases on transcription regulatory regions of eukaryotic genes and TRRD Viewer for data visualization; (2) Site Activity Prediction (ACTIVITY), the module for analysis of functional site activity and its prediction; (3) Site Recognition module, which comprises (a) B-DNA-VIDEO system for detecting the conformational and physicochemical properties of DNA sites significant for their recognition, (b) Consensus and Weight Matrices (ConsFrec) and (c) Transcription Factor Binding Sites Recognition (TFBSR) systems for detecting conservative contextual regions of functional sites and their recognition; (4) Gene Networks (GeneNet), which contains an object-oriented database accumulating the data on gene networks and signal transduction pathways, and the Java-based Viewer for exploration and visualization of the GeneNet information; (5) mRNA Translation (Leader mRNA), designed to analyze structural and contextual properties of mRNA 5'-untranslated regions (5'-UTRs) and predict their translation efficiency; (6) other program modules designed to study the structure-function organization of regulatory genomic sequences and regulatory proteins. AVAILABILITY: GeneExpress is available at http://wwwmgs.bionet.nsc. ru/systems/GeneExpress/ and the links to the mirror site(s) can be found at http://wwwmgs.bionet.nsc.ru/mgs/links/mirrors.html+ ++.

[WWWMGS: an integrated server for molecular-genetic studies]. / WWWMGS: integrirovannyi server dlia molekuliarno-geneticheskikh issledovanii.

We report an integrative technology for molecular biology studies in the field of transcription regulation by using Internet. A set of databases, programs, and systems are included into WWWMGS Web server. For example, the use of TRRD database information for site prediction is described. Using this method, the computer system SeqAnn was developed. The system performs the "real time" searching for prediction of initiation transcription site position according to database information. WWWMGS is available at URL: http://wwwmgs.bionet.nsc.ru/.

Object-oriented data handler for sequence analysis software development.

We report an object-oriented data handler and supplementary tools for the development of molecular genetics application software for various sequence analyses. Our data handler has a flexible and expandable format that supports the most common data types for molecular genetic software. New data types can be constructed in an object-oriented manner from the basic units. The data handler includes an object library, a format-converting program and a viewer that can visualize simultaneously the data contained in several files to construct a general picture from separate data. This software has been implemented on an IBM PC-compatible personal computer.