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Complex Trait Consortium Meeting, Oxford 1-3 July 2003 Sequence Alignment with ARIADNE Sequence Alignment with monotonic gap penalties Aligning an EST to a genomic sequence
BIOSAPIENS Network of Excellence Integrated Genotyping System (IGS)
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DNA-protein Binding PageThis page contains resources related to a project to predict the binding affinity of DNA-Protein interactions, as a function of the DNA sequence. We have developed a new method that identifies interactions between base pair positions in the binding site. It is described in detail here in PNAS (2002) 99:8167-8172. The work is a collaboration with Irina Udalova and Dominic Kwiatkowski . This page is still under construction. AbstractWe describe a general method based on principal coordinates analysis to predict the effects of single nucleotide polymorphisms within regulatory sequences on DNA-protein interactions. We use binding data for the transcription factor NF-kB as a test system. The method incorporates the effects of interactions between base pair positions in the binding site, and we demonstrate that such interactions are present for NF-kB. Prediction accuracy is higher than with profile models, confirmed by cross-validation and by the experimental verification of our predictions for additional sequences. The binding affinities of all potential NF-kB sites on human chromosome 22, together with the effects of known SNPs, are calculated to determine likely functional variants. We propose that this approach may be valuable, either on its own or in combination with other methods, when standard profile models are disadvantaged by complex inter-nucleotide interactions. Download Raw Data (Excel Spreadsheet) Download R functions to perform analysis (Currently undocumented) Click here for web server access to software to
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