NCBI Eukaryotic Genomes: Current Status, New Reports, and Annotation Summary

The NCBI eukaryotic genome annotation pipeline generates whole genome annotation results for plant and animal genomes for which the assembly (in public sequence archives) meets simple minimal quality thresholds. The pipeline was updated in 2013 to increase throughput, to incorporate use of RNA-Seq data, and to produce RNA-Seq tracks that are initially made available in the Gene resource. We annotated 65 eukaryotic genomes in the first 11 months of 2013 and the addition of RNA-Seq data significantly increased our representation of alternative splice variants due to a corresponding policy change such that a given gene may now be represented by both model RefSeqs produced by the annotation pipeline (XM, XR, XP accessions), and known RefSeqs supported by NCBI curation staff (NM, NR, NP accessions).  In addition to provision of genome annotation, RefSeq transcript and protein products, and gene calls, the pipeline also produces BLAST databases, FTP reports, and web reports. The eukaryotic annotation status web site (www.ncbi.nlm.nih.gov/genome/annotation_euk/status/) summarizes recently annotated and ‘in progress’ genome annotation runs, and a new detailed annotation report page summarizes the input datasets used and the annotation results per annotation build run.  This presentation will provide an overview of the annotation pipeline products and reports and will include examples of RNA-Seq based annotation as well as the new annotation report page.  The presentation will also summarize the current number, status, and data availability for plant and animal genome sequencing projects.