Update on NCBI's Eukaryotic Genome Annotation Pipeline and Expansion to Process RNA-Seq Data

The NCBI eukaryotic genome annotation pipeline provides content for several NCBI resources including RefSeq genome annotation, RefSeq predicted transcript and protein models, BLAST databases, Gene content, and the Map Viewer genome browser.  The annotation pipeline is largely automated from the initial retrieval of genome sequence data from the Assembly database, to calculating and interpreting sequence alignments, providing validation and QA reports, and providing final genome annotation results that are integrated with RefSeq and Gene data.  The pipeline has been designed to annotate multiple organisms in parallel, with run times in the range of 1-5 days. Using assembly-assembly alignments, the pipeline can annotate in coordination multiple assemblies for an organism, thereby ensuring consistent annotation and gene naming across assemblies from different sources.  The process flow incorporates logic to track gene annotations from one annotation run to another and gives greater weight to curated data inputs from the RefSeq project. The final annotation product can include transcripts and proteins for which the sequence has been modified relative to the draft genome assembly in order to correct a truncating mismatch or frameshift and represent a more complete protein.  The pipeline is now being expanded to include use of RNA-seq data in calculating transcript and protein annotations.  Integration of these datasets is expected to improve annotation of genomes which lack significant traditional transcript data.  This presentation will provide an overview of the annotation pipeline, our approach to integrate RNA-seq data, and how to access, use, and evaluate the quality of the final annotation products.