Thomas Abeel
,
VIB Ghent University, Ghent, Belgium
Stephane Rombauts
,
VIB Department of Plant Systems Biology, Ghent University, Ghent, Belgium
Yao-Cheng Lin
,
VIB Department of Plant Systems Biology, Ghent University, Ghent, Belgium
Pierre Rouzé
,
VIB Ghent University, Department of Plant Biotechnology and Bioinformatics, Ghent, Belgium
Yves Van de Peer
,
VIB - Ghent University, Zwijnaarde, Belgium
Conducting gene and genome annotation typically relies on diverse information resources going from sequence (eg. transcript and protein alignments) to expression data (eg. read count analysis) depending on whether structural or functional annotation is performed. To help researchers doing gene annotation while having access to these different data types, we developed ORCAE, a web-technology-compliant portal for use in community genome annotation efforts.
ORCAE allows browsing and on the fly editing of gene descriptions as well as gene structures. Moreover, all manual curations are immediately visible for other users and for each locus a history of modifications is available. Through its interface, ORCAE offers access to precomputed information that greatly facilitates the work of a curator. The gene page includes several informative graphics, with a focus on the quality of gene structures (eg. multiple alignments of homologs), helping the human annotators in improving the proposed automated annotation. Annotators can thus easily check/modify gene structures with the build-in GenomeView interface. A unique feature from ORCAE is that the portal is highly dynamic. On modification of a gene model, all the available information (eg. protein similarity, transcript alignments, etc.) is immediately updated and presented on the gene page.
ORCAE can both be used to coordinate annotation efforts in the course of the project as well as to present published genomes to the public by acting as a public genome browser/portal. Currently it offers public access to 12 eukaryotic genome projects and restricted access to another 11 genomes.
