Objective
Sequencing of bacterial genomes has created both a challenge and an opportunity for bioinformatics. It is a challenge because the genome sequencing rate exceeds the capacity of manual annotation, and it is an opportunity because it allows one to use comparative techniques for genome annotation, and to study function and evolution of metabolic pathways and regulatory systems and, eventually, complete genomes. The main technical objectives of this project are development and integration of methods for functional annotation of genomes, including gene recognition, functional annotation of genes, identification of regulatory signals; comparative approaches to metabolic reconstruction; tools for genome alignment and synteny analysis, and application of the developed software for analysis of concrete genomes. The fundamental research will be directed towards evolution of genomes, metabolic pathways and regulatory systems, with particular attention on: metabolic systems subject to complex regulation by multiple interacting systems; taxon-specific regulation and microevolution of regulons and regulatory sites; and structural properties and evolution of regulatory protein-DNA interactions. We will also continue manual analysis of selected metabolic pathways and regulatory systems, leading to annotation of new protein functions and identification of regulatory signals, with special attention towards prediction of transporter specificity. We will attempt to formulate models of evolution of regulatory sites, regulons (sets of co-regulated genes) and regulatory systems. The proposed research combines main aspects of contemporary bioinformatics, from application of probability theory to algorithm development, software implementation, and analysis of real data, and from genome sequence analysis to structural studies. All teams have strong background in bioinformatics and, in particular, in comparative genomics. The consortium members collaborate since 1999. In 2000-2002 several teams collaborated in the INTAS project 99-1476, and the developed methods and algorithms will be used as research tools in the present project. The research program requires tight integration between the participating teams. The created software will be immediately used for genome analysis, and the provided users' feedback will be taken into account in subsequent releases. Analysis of metabolic and regulatory systems will create data for large-scale functional, structural, and evolutionary studies. Conversely, understanding of general principles of metabolic and regulatory evolution will lead to creation of better tools for functional annotation. Thus the proposed project will result both in development of tools for genome analysis and, specifically, prediction of bacterial phenotype (metabolic capabilities, regulation, response to stress and external stimuli) from genomic data, and deeper understanding of all aspects of genome structure, function and evolution.
Fields of science (EuroSciVoc)
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Keywords
Project’s keywords as indicated by the project coordinator. Not to be confused with the EuroSciVoc taxonomy (Fields of science)
Project’s keywords as indicated by the project coordinator. Not to be confused with the EuroSciVoc taxonomy (Fields of science)
Programme(s)
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Multi-annual funding programmes that define the EU’s priorities for research and innovation.
Topic(s)
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Calls for proposals are divided into topics. A topic defines a specific subject or area for which applicants can submit proposals. The description of a topic comprises its specific scope and the expected impact of the funded project.
Call for proposal
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Procedure for inviting applicants to submit project proposals, with the aim of receiving EU funding.
Funding Scheme
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Funding scheme (or “Type of Action”) inside a programme with common features. It specifies: the scope of what is funded; the reimbursement rate; specific evaluation criteria to qualify for funding; and the use of simplified forms of costs like lump sums.
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Coordinator
FREISING
Germany
The total costs incurred by this organisation to participate in the project, including direct and indirect costs. This amount is a subset of the overall project budget.