Missouri Botanical Garden Open Conference Systems, TDWG 2013 ANNUAL CONFERENCE

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Quest for Orthologs: anchoring comparative biology research
Suzanna Lewis, Quest for Orthologs Consortium

Building: Grand Hotel Mediterraneo
Room: America del Nord (Theatre I)
Date: 2013-10-31 09:55 AM – 10:05 AM
Last modified: 2013-10-05

Abstract


Quest for Orthologs (QfO) is a volunteer effort to jointly create a firmer foundation for comparative biology research. Extrapolating knowledge from a handful of organisms for which experimental data is available to other living organisms is the heart of comparative biology, and orthology assignments are axiomatic. Whether the aim is to find the gene in a model organism corresponding to a human disease gene, inferring the function of a newly sequenced gene using available experimental assays from its orthologs, or inferring species phylogenies by tracing the evolution of orthologous groups, reliable ortholog predictions are needed. Any improvement to this essential base will offer enormous benefit to the entire biological community. Currently more than 30 different phylogenomic databases provide their ortholog analysis results to the scientific community, each differing in many ways—number of species, taxonomic range, sampling density, applied methodology, and more. In addition, phylogenomic databases differ in their concepts, making direct benchmarking problematic and presenting major obstacles to the user community looking for relationships between genes.

One of the prerequisite for the QfO consortium is a shared species phylogeny, which is used for the final determination of gene relationships during construction of sequence-based gene trees. A cladogram was therefore constructed for the 147 species of the reference proteomes (http://www.ebi.ac.uk/reference_proteomes/) based on information from various resources (http://wiki.isb-sib.ch/swisstree/Species_tree_for_Quest_for_Orthologs_reference_proteomes_2013). This talk will present the current progress by the QfO consortium and ideally lead to a discussion of common needs and open questions.