Prediction of eukaryotic mRNA translational properties.

MOTIVATION: It is well known that eukaryotic mRNAs are translated at different levels depending on their sequence characteristics. Evaluation of mRNA translatability is of importance in prediction of the gene expression pattern by computer methods and to improve the recognition of mRNAs within cloned nucleotide sequences. It may also be used in biotechnological experiments to optimize the expression of foreign genes in transgenic organisms. RESULTS: The sets of 5' untranslated region characteristics, significantly different between mRNAs encoding abundant and scarce polypeptides, were determined for mammals, dicot plants and monocot plants, and collected in the LEADER_RNA database. Computer tools for the prediction of mRNA translatability are presented. AVAILABILITY: Programs for mRNA translatability prediction are available at http://wwwmgs.bionet.nsc. ru/programs/acts2/mo_mRNA.htm (for monocots), http://wwwmgs.bionet. nsc.ru/programs/acts2/di_mRNA.htm (for dicots) and http://wwwmgs. bionet.nsc.ru/programs/acts2/ma_mRNA.htm (for mammals). The LEADER_RNA database may be accessed at: http://wwwmgs.bionet.nsc. ru/systems/LeaderRNA/.     

Gene Network and Database for Genes of Wheat’s Resistance to Pathogenic Fungi

An overview describing a gene network that controls the formation of plant responses to diseases caused by pathogenic fungi (http://wwwmgs.bionet.nsc.ru/mgs/gnw/genenet//viewer/Plant%20fungus%20pathogen.html) is presented. The gene network represents the coordinated interactions of genes, proteins, and regulatory molecules, including integrated defense mechanisms that prevent the development of infection, localize the lesion, and minimize damage. The gene network was reconstructed on the basis of literature data, and the elements of the gene network were associated with the records of the PGR database (Pathogenesis-Related Genes, http://srs6.bionet.nsc.ru/srs6bin/cgi-bin/wgetz?-page+top+-newId), where information on plant genes resistant to pathogenic fungi is accumulated. Reconstruction of the gene network allows us to formalize, visualize, and systematize possible mechanisms for the response of plant cells to fungal infection, which may be useful for the planning of experiments and interpretation of experimental data in this field of science.     

Integrated computer system for regulating eukaryotic gene expression

The review describes several modules of the GeneExpress integrated computer system concerning the regulation of gene expression in eukaryotes. Approaches to the presentation of experimental data in databases are considered. The employment of GeneExpress in computer analysis and modeling of the organization and function of genetic systems is illustrated with examples. GeneExpress is available at http://wwwmgs.bionet.nsc.ru/mgs/gnw/.     

An Integrated Computer System for Studying the Regulation of Eukaryotic Gene Expression

The review describes several modules of the GeneExpress integrated computer system concerning the regulation of gene expression in eukaryotes. Approaches to the presentation of experimental data in databases are considered. The employment of GeneExpress in computer analysis and modeling of the organization and function of genetic systems is illustrated with examples. GeneExpress is available at http://wwwmgs.bionet.nsc.ru/mgs/gnw/.     

A systems approach to morphogenesis in Arabidopsis thaliana: I. AGNS database

In systems biology, study of a complex and multicomponent system, such as morphogenesis, comprises accumulation of data on morphogenetic processes in databases, classification and logical analysis of this information, and computer simulation of the processes in question using the data accumulated and the results of their analysis. This paper describes realization of the first steps in a systems study of morphogenesis (annotating research papers, compiling information in a database, data systematization, and their logical analysis) by the example of Arabidopsis thaliana, a model object in plant molecular biology. The database AGNS (Arabidopsis GeneNet Supplementary; http://wwwmgs.bionet.nsc.ru/agns) contains the experimentally confirmed information from published papers on specific features of gene expression and phenotypes of wild-type, mutant, and transgenic A. thaliana plants. AGNS queries and logical data analysis with the aid of specially developed software makes it possible to model various morphogenetic processes from gene expression to functioning of gene networks and their contribution to the development of certain traits.

     

Interstitial telomeric repeats as markers of evolutionary changes in the mammalian karyotype: Human chromosome 2

The presence of conserved telomeric repeats represented by the hexamer (TTAGGG)_n at the chromosomal termini is necessary for the correct functioning and stability of chromosomes. A number of the genomes of mammals, including human, are known to contain interstitial telomeric sequences located far from the chromosomal termini. It is assumed that these repeats mark the regions of fusions or other rear-rangements of ancestral chromosomes. Exact localization of all interstitial telomeric sequences in the genome could significantly advance the understanding of the mechanisms of karyotype evolution and speciation. In this context, software was developed to search for degenerate interstitial telomeric repeats in complete sequences of mammalian chromosomes. The evolutionary significance of such repeats was demonstrated by the example of human chromosome 2. The results are available at http://www.bionet.nsc.ru/labs/theorylabmain/orlov/telomere/.     

Prediction of contact numbers of amino acid residues using a neural network regression algorithm

The profile of contact numbers of amino acid residues in proteins contains important information about the protein structure and is connected with the accessibility of residues to solvent. Here we propose a method for predicting the profile of contact numbers of residues in protein from its amino acid sequence. The method is based on regression using a neural network algorithm. The algorithm predicts two types of profiles, namely, the total number of contacts and the number of close contacts with the neighbors in the chain. The Pearson coefficient of correlation between the actual and predicted values of total contact numbers amounted to 0.526–0.703. As for the number of close contacts, this coefficient was higher (0.662–0.743) for all the considered threshold contact distances (6, 8, 10, and 12 Å). The program for prediction of contact numbers CONNP is available at http://wwwmgs2.bionet.nsc.ru/reloaded.

     

An Algorithm of Step-by-step Pedigree Drawing

An algorithm for drawing large, complex pedigrees containing inbred loops and multiple-mate families is presented. The algorithm is based on a step-by-step approach to imaging, when the researcher determines the direction of further extension of the scheme. The algorithm is implemented as the PedigreeQuery software package written in Java. The software has a convenient graphical interface. The software package permits constructing not only whole pedigrees, but also their fragments that are particularly interesting for research. It also allows for adding new information on the phenotypes and genotypes of pedigree members. PedigreeQuery is distributed free of charge; it is available at http://mga.bionet.msc.ru/PedigreeQuery/PedigreeQuery.html and ftp://mga.bionet.nsc.ru/PedigreeQuery/.     

Analysis and recognition of promoters for erythroid-specific genes based on degenerative oligonucleotide motifs]

We developed a method to search for degenerate oligonucleotide motifs specific for certain regions in eukaryotic gene promoters. A procedure of promoter recognition based on these motifs is presented. The methods are integrated within program package ARGO available for the Internet users (http://wwwmgs.bionet.nsc.ru/mgs/programs/argo). This method was applied to study erythroid-specific gene promoters. High efficiency of their recognition is demonstrated.     

Analysis and Recognition of Erythroid-Specific Gene Promoters Basing on Degenerate Oligonucleotide Motifs

We developed a method to search for degenerate oligonucleotide motifs specific for certain regions in eukaryotic gene promoters. A procedure of promoter recognition based on these motifs is presented. The methods are integrated within the program package ARGO available for Internet users (http://wwwmgs.bionet.nsc.ru/mgs/programs/argo). This method was applied to study erythroid-specific gene promoters. High efficiency of their recognition is demonstrated.