W049 Churchillian wisdom in fish genome annotation

Date: Sunday, January 15, 2012
Time: 8:20 AM
Room: Royal Palm Salons 3-4
Shane Burgess , College of Agriculture and Life Sciences, University of Arizona, Tucson, AZ
Annotation is the essential step in genomics after sequencing and sequence assembly; without annotation a genome sequence is represented only by billions of “A’s, C’s, G’s and T’s” in a string. Genome annotation has two components: 1. Structural, which is the delineation and demarcation of functional elements within the genome and 2. Functional,  which is describing genomic elements in terms of their functions. In both cases ontologies have become essential tools and community involvement invaluable. Furthermore, gene nomenclature is critical, and sometimes controversial,  in both structural and functional annotation. Some key elements in genome annotation include the need for experimental confirmation of open reading frames (ORFs) predicted during genome assembly and the use of the Sequence Ontology for sequence annotation. In functional annotation, the primary ontology used is the Gene Ontology (GO; which has three components: Biological Process, Molecular Function and Cell Component), many predicted ORFs will have no functional literature and GO annotation relies on computation methods and the fact that functional literature exists for many genes/proteins prior to genome sequencing meaning that GO-base annotation does not rely on a completed genome sequence and that functional annotation provides the basis for biological modeling. I will summarize what we and others have found during genome annotation projects so aquatic species genome communities may potentially benefit from other's experiences.