EAGER: Improved Computational Tools for Plant Gene Assembly and Synteny Detection

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The ever-increasing rate of genome sequence production will result in literally thousands of genome sequences being determined. Current automated methods for plant gene assembly have certain inherent weaknesses that result in many incorrectly assembled genes due to inaccurate detection of true intron-exon boundaries including GC boundaries, inability to detect N-terminal exons, and inappropriate fusion of adjacent genes. Expert manual annotation can usually overcome these limitations, but manual annotation is not scalable to many thousands of genes. Genome projects generally are able to claim only 1000-3000 genes were manually checked. In plant genomes this may be only 3-10% of the genes in the genome. This EAGER project seeks to improve automated plant gene assembly and annotation with a focus on cytochrome P450 genes, which comprise one of the largest gene families in plants. Successful implementation of accurate gene prediction algorithms and the development of a novel tool for identifying ohnologs (genes created by whole genome duplication events) in plant genomes will have a transformative effect on genome annotation.This project will provide international cross-disciplinary training opportunities for one postdoctoral research associate. All programs will be available as a set of executable files from an ftp site and through the project website, both of which will be accessible via http://www.uthsc.edu/molecular_sciences/directories/faculty/d_nelson.php. The source code will also be made available at this location.