Developing an Integrated Toolkit to Explore Code/Genome Interaction

University Of Maryland Baltimore County, Baltimore MD

Investigators

Abstract

The University of Maryland Baltimore County has been given a grant to engage collaborative student teams (comprising Biologists and Computer Scientists) in developing integrated, web-based software improving algorithms for homology detection, optimizing synthetic gene design and predicting protein structure from sequence data. The software will generate detailed predictions of (i) the relative rates at which amino acids interchange over evolutionary time; (ii) the optimal encoding of any given gene within any given genome; and (iii) the a priori reasons why patterns of synonymous codon usage vary within genes according to the protein secondary structures that they encode. The toolkit will use computing techniques such as integrated XML data objects constructed by CGI query of specialized databases and SOAP wrapper integration of modular algorithms delivered as web services.