| EPSRC Reference: |
GR/S60266/01 |
| Title: |
Context information augmented DNA sequencing |
| Principal Investigator: |
Gillies, Professor D |
| Other Investigators: |
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| Project Partners: |
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| Department: |
Computing |
| Organisation: |
Imperial College London |
| Scheme: |
Standard Research (Pre-FEC) |
| Starts: |
01 October 2003 |
Ends: |
31 March 2007 |
Value (£): |
217,353
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| EPSRC Research Topic Classifications: |
| Bioinformatics |
Information & Knowledge Mgmt |
| Software Engineering |
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| EPSRC Industrial Sector Classifications: |
| Healthcare |
Information Technologies |
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| Panel History: |
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Summary on Grant Application Form |
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We have proposed a new method of interpreting DNA sequencing traces using computational analysis of the biochemical and physical systems used to generate them. This analysis shows that peak height variation contains important information that can be used to provide more accurate base calls than are currently made. We have modelled the factors that determine peak height numerically. In collaboration with the Wellcome Trust Sanger Institute, we will calibrate the model using traces from DNA sequences we design and build for optimal efficiency. The calibrated models can be used to estimate the trace data that would arise from any DNA sample composition. A full sequence can be determined starting from a set of hypothesised fragments which are grown appropriately. This research will synthesize a hypothesis navigation scheme which uses comparisons between predicted and measured trace data, calculating the likelihood of each hypothesised sequence, and guiding the most effective hypothesis growth. This scheme will thus efficiently traverse the space of possible sample sequence compositions, enabling more effective interpretation. The improved accuracy will benefit researchers in applied computer science fields such as bioinformatics and molecular modelling, and in the life sciences - for example in determining the aetiology of disease. exposing cell mechanisms. and providing better diagnostic tests.
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Key Findings |
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This information can now be found on Gateway to Research (GtR) http://gtr.rcuk.ac.uk
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Potential use in non-academic contexts |
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This information can now be found on Gateway to Research (GtR) http://gtr.rcuk.ac.uk
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Impacts |
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| Description |
This information can now be found on Gateway to Research (GtR) http://gtr.rcuk.ac.uk |
| Summary |
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| Date Materialised |
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Sectors submitted by the Researcher |
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This information can now be found on Gateway to Research (GtR) http://gtr.rcuk.ac.uk
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| Project URL: |
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| Further Information: |
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| Organisation Website: |
http://www.imperial.ac.uk |