POGs/PlantRBP: A resource for comparative genomics in plants

Abstract

POGs/PlantRBP (http://plantrbp.uoregon.edu/) is a relational database that integrates data from rice, Arabidopsis, and maize by placing the complete Arabidopsis and rice proteomes and available maize sequences into 'putative orthologous groups' (POGs). Annotation efforts will focus on predicted RNA binding proteins (RBPs): i.e. those with known RNA binding domains or otherwise implicated in RNA function. POGs form the heart of the database, and were assigned using a mutual-best-hit-strategy after performing BLAST comparisons of the predicted Arabidopsis and rice proteomes. Each POG entry includes orthologs in Arabidopsis and rice, annotated with domain organization, gene models, phylogenetic trees, and multiple intracellular targeting predictions. A graphical display maps maize sequences on to their most similar rice gene model. The database can be queried using any combination of gene name, accession, domain, and predicted intracellular location, or using BLAST. Useful features of the database include the ability to search for proteins with both a specified domain content and intracellular location, the concurrent display of mutual best hits and phylogenetic trees which facilitates evaluation of POG assignments, the association of maize sequences with POGs, and the display of targeting predictions and domain organization for all POG members, which reveals consistency, or lack thereof, of those predictions. © 2007 Oxford University Press.