Suggestions & Proposals
Centre for Bioengineering RAS, Moscow:
1. Development of dynamic model of development of a flower.
In this investigation the studying literary data on interaction of genes during a flower developing is spent and on the basis of this studying the dynamic model of a flower morphogenes is developed. Petri net will be developed for creation of dynamic model of flower morphogenesis. Petri net permits to model interactions of known genes during flower developing. Dynamic Petri net will receive unequivocal visualization which will allow to build on a course of Petri net work the image of development of a flower on the screen. The created software will allow to transform Petri net in conformity with interaction of genes, presence of mutations and thus to receive the forecast of development of a flower. It is important for reception of forecasts of development of a flower at presence of the mutant genes changing character of intergenic interaction. The developed software as a result of performance of the project has universal character and will represent a workplace of the genetic engineer which is modelling various genetic processes by Petri net in a dynamic mode.
2. A databank potential mini and microsatellite DNA sequences.
Earlier in the Center "Bioengineering" of the Russian Academy of Science the method of information decomposition of the symbolical sequences has been developed, allowing to find out various periodic sequences from defferent genomes. The most part of these sequences it is impossible to find out other developed mathematical approaches and algorithms. The method of information decomposition will analyse all Genbank and all potential mini and microsatellite sequences will be revealed in view of an opportunity of indels. The databank potential mini and microsatellites will contain the following information. 1 DNA sequences with the found periodicity and itscoordinates in corresponding locus of Genbank; 2. parameters of the found periodicity and its type. The databank will contain some millions potential mini and microsatellite sequences. Found types of mini and microsatellite DNA sequences will be classified and Web-site for detection of mini and microsatelite sequences in DNA sequences will be created.
3. Developing of computer system for biological function of amino acid sequence annotation.
New methods of the Information Decomposition (ID), Noise Decomposition (ND) and Modified Profile Analysis (PMA) have found that 200 protein families contain a latent periodicity that is specific for a protein family and for biology function of a protein family. In this work we are going to investigate the presence of latent periodicity additionally in more than 3000 protein families and domains, modify the ID method for search of latent periodicity with presence of deletions and insertions (indels) and develop of data bases of amino acid sequences from different protein families with latent periodicity. As result the new method for prediction (annotation) of biology function of amino acid sequences will be developed on base of presence of certain type of the latent periodicity in the amino acid sequences. Specific arms of the project are:
A. Using the Information Decomposition (ID), Noise Decomposition (ND) methods show the presence of a specific latent periodicity in more than 3000 different protein families and domains;
B. Create the data bank where latent periodicity of the amino acid sequences from more than 3000 protein families will be present
C. Develop the modification of ID method with help of dynamic programming method for search of a latent periodicity in amino acid sequence with deletions and insertions.
D. Create new software for the prediction of biological function of amino acid sequences (for biological functions more than 3000 investigated protein families) with help of found latent periodicity. Creation of Web-site for annotation of biological function of amino acid sequences for any user.
4. Study of repeats in plants genomes and investigation of chromosome evolution.
The purpose of work is creation of new information resources for researches of the plant genomes of Arabidopsis thaliana and Oriza sativa. During researches all copies of SINE and LINE repeats that are typical for plant genomes of A.thaliana and O.sativa will be revealed. On the basis of these data the database on SINE and LINE repeats will be created. Then development of algorithm of classification of plant repeats will be lead. We also shall create a mathematical method for development of algorithm of an estimation of evolutionary similarity of chromosomes on the basis of repeat classes. As a result of research the scheme of probable evolution of chromosomes for A.thaliana and for O.sativa genomes will be constructed. Testing hypothesis of Ohno About evolution of genes by duplication and divergency of ancient olygous for an example genomes A.thaliana and O.sativa will be lead.
5. Education in bioinformatics and system biology.
Centre of Bioiengineering of RAS can take Ph-D students for study in bioinformatics. For work in bioinformatics and system biology we have computer cluster with 96 processors. Student can execute their diploma and Ph.D.work for
time from 0.5 year for 3 years.
List of publications:
1. Alexeev DV, Ezhova TA, Kozlov VN, Kudriavtsev VB, Nosov MV, Penin AA, Skriabin KG, Choob VV, Shulga OA, Shestakov SV. Related Articles, Spatial pattern formation in the flower of Arabidopsis thaliana: mathematical modeling. Dokl Biol Sci. 2005 v.401:133-135.
2. Chaley M.B., Korotkov E.V., Kudryashov N.A. Latent Periodicity of 21 bases Typical for MCP II Gene is Widely Present in Various Bacterial Genes.// DNA Sequence, v.14, 37-52,2003.
3. Frenkel F.E., Chaley M.B., Korotkov E.V., Skryabin K.G. "Evolution of the tRNA-like sequences and genome variability" Gene, v.335C: 57-71, 2004.
4. Laskin AA, Kudryshov NA, Korotkov EV "Noise decomposition method and its application for search of latent periodicity in protein kinases", Molecular Biology, (Russian), N3, 420-436. 2005.
5. Laskin AA, Kudryashov NA, Skryabin KG, Korotkov EV. Latent periodicity of serine-threonine and tyrosine protein kinases and other protein families. Comput Biol Chem. 2005 29(3):229-243
6. Turutina VP, Laskin AA, Skryabin K.G., Kudryashov N.A. and Korotkov EV, "Latent periodicity of many protein families", Biochemistry, 2006, 71, 18-31.
7. Turutina VP, Laskin AA, Skryabin K.G., Kudryashov N.A. and Korotkov EV, "Latent periodicity of 94 protein families", J. Compt. Biol. V.13, 946-964, 2006 .