Update on the Eukaryotic Genome Annotation Pipeline

The NCBI Eukaryotic Genome Annotation Pipeline (www.ncbi.nlm.nih.gov/genome/annotation_euk/) provides content for various NCBI resources including RefSeq sequence databases, Gene, BLAST databases and the Map Viewer genome browser. As of November 1st, 2014 the pipeline has been used to annotate over 180 organisms, 100 of them with the help of RNA-Seq data.

The pipeline uses a modular framework for the automated execution of all annotation tasks. Core components of the pipeline are the Splign and ProSplign alignment programs and Gnomon, an alignment- and HMM-based gene prediction program, developed at NCBI.

High-quality annotation is achieved in part by weighting RefSeq curated evidence more heavily than non-curated evidence, and by producing models that compensate for assembly issues. 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. In 2014, this notion was pushed farther with “gap-filling”, the utilization of aligned transcript sequences to improve the annotation of transcript and protein products that are only partially represented in the genome owing to sequence gaps. 

Improvements to the web reports generated with each annotation will also be shown. One signficant addition to these is the comparative evaluation of sets of annotated proteins based on BLAST alignments to a set of curated proteins (typically UniProtKB/SwissProt). Finally, we’ll report progress on the development of comparative reports for better understanding changes in annotation between two annotation releases.

See all NCBI-annotated eukaryotes at: http://www.ncbi.nlm.nih.gov/genome/annotation_euk/all/