Roos, David S
Email Address
ORCID
Disciplines
Search Results
Now showing 1 - 2 of 2
Publication Reranking candidate gene models with cross-species comparison for improved gene prediction(2008-10-14) Liu, Qian; Crammer, Koby; Roos, David S; Pereira, Fernando CNBackground: Most gene finders score candidate gene models with state-based methods, typically HMMs, by combining local properties (coding potential, splice donor and acceptor patterns, etc). Competing models with similar state-based scores may be distinguishable with additional information. In particular, functional and comparative genomics datasets may help to select among competing models of comparable probability by exploiting features likely to be associated with the correct gene models, such as conserved exon/intron structure or protein sequence features. Results: We have investigated the utility of a simple post-processing step for selecting among a set of alternative gene models, using global scoring rules to rerank competing models for more accurate prediction. For each gene locus, we first generate the K best candidate gene models using the gene finder Evigan, and then rerank these models using comparisons with putative orthologous genes from closely-related species. Candidate gene models with lower scores in the original gene finder may be selected if they exhibit strong similarity to probable orthologs in coding sequence, splice site location, or signal peptide occurrence. Experiments on Drosophila melanogaster demonstrate that reranking based on cross-species comparison outperforms the best gene models identified by Evigan alone, and also outperforms the comparative gene finders GeneWise and Augustus+. Conclusion: Reranking gene models with cross-species comparison improves gene prediction accuracy. This straightforward method can be readily adapted to incorporate additional lines of evidence, as it requires only a ranked source of candidate gene models.Publication Local Admixture of Amplified and Diversified Secreted Pathogenesis Determinants Shapes Mosaic Toxoplasma gondii Genomes(2016-01-01) Lorenzi, Hernan; Kahn, Asis; Behnke, Michael S; Namasivayam, Sivaranjani; Pinney, Deborah; Swapna, Lakshmipuram S; Brunk, Brian P.; Hadjithomas, Michalis; Karamycheva, Svetlana; Ajioka, James W; Ajzenberg, Daniel; Boothroyd, John C; Boyle, Jon P; Dardé, Marie; Diaz-Miranda, Marie A; Gregory, Brian D; Dubey, Jitender P; Fritz, Heather M; Gennari, Solange M; Kim, Kami; Saeij, Jeroen PJ; Su, Chunlei; White, Michael W; Zhu, Xing-Quan; Howe, Daniel K; Rosenthal, Benjamin M; Grigg, Michael E; Roos, David S; Parkinson, John; Liu, Liang; Kissinger, Jessica C; Sibley, L. DToxoplasma gondii is among the most prevalent parasites worldwide, infecting many wild and domestic animals and causing zoonotic infections in humans. T. gondii differs substantially in its broad distribution from closely related parasites that typically have narrow, specialized host ranges. To elucidate the genetic basis for these differences, we compared the genomes of 62 globally distributed T. gondii isolates to several closely related coccidian parasites. Our findings reveal that tandem amplification and diversification of secretory pathogenesis determinants is the primary feature that distinguishes the closely related genomes of these biologically diverse parasites. We further show that the unusual population structure of T. gondii is characterized by clade-specific inheritance of large conserved haploblocks that are significantly enriched in tandemly clustered secretory pathogenesis determinants. The shared inheritance of these conserved haploblocks, which show a different ancestry than the genome as a whole, may thus influence transmission, host range and pathogenicity.