To infer gene functions for a multitude of species, we have developed a highly accurate and computationally efficient method for large-scale applications of high-throughput orthology predictions. The method contains three major steps: 1) all-against-all gene comparisons for every pair of genes, 2) pair-wise orthology predictions for every two genomes, and 3) the generation of orthologous clusters that contain orthologous genes across multiple genomes. Our database currently contains predicted orthologs for over 900 bacterial genomes.
Yu, C., V. Desai, L. Cheng, and J. Reifman. QuartetS-DB: a large-scale orthology database for prokaryotes and eukaryotes inferred by evolutionary evidence. BMC Bioinformatics. 2012 June 22; 13:143. [PDF 2459 KB]
Yu, C., N. Zavaljevski, V. Desai, and J. Reifman. QuartetS: a fast and accurate algorithm for large-scale orthology detection. Nucleic Acids Research. 2011 May 13; 39(13):e88. [PDF 361 KB]
Yu, C., V. Desai, N. Zavaljevski, and J. Reifman. Large-scale orthology predictions for inferring gene functions across multiple species. Proceedings of the HPCMP Users Group Conference. Schaumburg, IL. 2010 June 14-17; 269-272. [PDF 170 KB]
Yu, C., and P. A. Wilson. A tool for creating and parallelizing bioinformatics pipelines. Proceedings of the HPCMP Users Group Conference. Pittsburgh, PA. 2007 June 18-22; 417-420. [PDF 769 KB]