A Database of Fungal Protein Clusters for Comparative Genomics

Jung, J., Yi, G., Sukno, S.A. and Thon, M.R. 25th Fungal Genetics Conference, Asilomar, CA, USA. March 17-22, 2009.

The Fungal Protein Cluster Database (FPC-DB) enables users to quickly locate information about the phylogeny and functional categories of fungal proteins and gene families and present the information in a number of comparative views. The proteins from fungal whole-genome sequencing projects are annotated with InterPro and Gene Ontology terms using an automated functional classification server previously developed in our group. The proteins are then clustered into putative gene families. Each protein cluster includes multiple sequence alignments, phylogenetic trees and a summary of functional categories found in the cluster. Users can perform queries using protein IDs, protein functional categories, and species names as search terms. The results are displayed in a variety of forms that allow users to compare the occurrence of gene and their functional categories between species. Users can also view a detailed page for each protein cluster and simultaneously view a phylogenetic tree and a matrix of functional categories. Comparative views enable users to directly compare gene family content between species to identify changes in gene family size between species.

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