Recent Updates in the Eukaryotic Genome Annotation Pipeline

The NCBI Eukaryotic Genome Annotation Pipeline (www.ncbi.nlm.nih.gov/genome/annotation_euk/) has been used to annotate over 260 organisms, ranging from plants to insects and mammals. The pipeline provides content for various NCBI resources including RefSeq sequence databases, Gene, BLAST databases and the Map Viewer genome browser.

The pipeline uses a modular framework for the automated execution of all annotation tasks from the fetching of raw and curated data from public repositories to the submission of the RefSeq-accessioned annotation products to public databases. The quality of the annotation is highly dependent on the availability of evidence for the species or closely related species. Alignments of RNA-Seq, traditional transcripts, ESTs, transcript assemblies and proteins by Splign and ProSplign all contribute to the prediction of gene models by Gnomon, an alignment- and HMM-based gene prediction program developed at NCBI. High-quality annotation is achieved also by weighting RefSeq curated evidence more heavily than non-curated evidence, and by producing models that compensate for assembly issues. The final products of the pipeline include the annotated genomic sequences, the genes, and the transcript and protein products named based on orthology to model organisms or Blast hits to SwissProt/UniProtKb.

We aim to re-annotate every organism we maintain every two years, so that the annotation incorporates recent evidence deposited in public databases, and benefits from improvements in the software. We will present a new type of report, to be published which each re-annotation, which categorizes the changes for each gene between two annotation releases.

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