AUTOMATED DETECTION OF REGIONS OF INTEREST IN MEMBRANE TRANSPORTERS

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This subproject is one of many research subprojects utilizing the resources provided by a Center grant funded by NIH/NCRR. The subproject and investigator (PI) may have received primary funding from another NIH source, and thus could be represented in other CRISP entries. The institution listed is for the Center, which is not necessarily the institution for the investigator. Previously, the NIH/GM-funded Pharmacogenetics of Membrane Transporters (PMT) research project restricted areas of single nucleotide polymorphism (SNP) discovery in membrane transporters to exons and short flanking sequences surrounding these exons, resulting in little leveraging of information available from other genome projects. However, by using conserved regions of sequence from other organisms surrounding the exon of interest additional insight can be gained into areas where functionally important SNPs may occur. Combining this information with repeat masking and graphical imaging allows for rapid visual detection of new SNP search spaces with a good prospect of successful PCR amplification. We are now extending a previous pilot study exploring this idea by automating the retrieval and processing of this information for 350 membrane transporters of interest.