Objective
The DNA molecule encodes the genetic information; reading the sequence it carries is of great relevance for biology and medicine. Currently available techniques are able to sequence DNA with high reliability but are very expensive in terms of time and human resources. We will focus on a new method for sequencing that is under intensive experimental investigation. The double helix of the DNA molecule is opened through a mechanical separation of the two strands, and the required force is measured. From the force signal one would like to reconstruct the DNA sequence.
The method is fast, but the force signal is very noisy and the reconstruction of the sequence turns out to be a difficult inference problem. A detailed comprehension of the noise and the design of optimal algorithms for data analysis are mandatory to achieve a reliable sequencing. The project will focus on the theoretical aspects of the method.
We will:
1) investigate the different sources of noise in the context of recent models for the DNA opening;
2) try to obtain theoretical bounds on the amount of information that can be obtained from the mechanical opening experiment as a function of the experimental parameters (resolution, total duration of the experiment, ...);
3) design efficient algorithms to optimise the data analysis in order to get as close as possible to the theoretical bounds;
4) test the algorithms against experimental data on known sequences and attempt to predict unknown sequences.
The project, if successful, will clearly establish the intrinsic limits of the method, in terms of information theory. Our results will be validated through a close collaboration with a leading experimental group in the field and, hopefully, will allow for a reliable mechanical sequencing in a not too far future. We believe that the project will enhance the EU competitivity in the thematic priorities 3 (nanosciences) and 1 (genomics) of the FP6.
Fields of science (EuroSciVoc)
CORDIS classifies projects with EuroSciVoc, a multilingual taxonomy of fields of science, through a semi-automatic process based on NLP techniques. See: The European Science Vocabulary.
CORDIS classifies projects with EuroSciVoc, a multilingual taxonomy of fields of science, through a semi-automatic process based on NLP techniques. See: The European Science Vocabulary.
- natural sciences computer and information sciences data science
- natural sciences biological sciences genetics DNA
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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)
Multi-annual funding programmes that define the EU’s priorities for research and innovation.
Multi-annual funding programmes that define the EU’s priorities for research and innovation.
Topic(s)
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.
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
Procedure for inviting applicants to submit project proposals, with the aim of receiving EU funding.
Procedure for inviting applicants to submit project proposals, with the aim of receiving EU funding.
FP6-2005-MOBILITY-5
See other projects for this call
Funding Scheme
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.
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.
Coordinator
PARIS
France
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.