Navigating the Annotated Horse Genome at NCBI

Genome annotation has become an important goal for the horse research community since an Equus caballus genome assembly became available. NCBI provides whole-genome annotation for the horse genome by a combination of manual curation and gene prediction. The annotations are available in Map Viewer, BLAST databases, Gene, RefSeq, and our ftp site. Additional resources support access and analysis of equine genome annotation, generated by NCBI or the research community. The recently updated Genome database provides species-level records with information about the organism, its genome structure, available assemblies and annotations, and related genome-scale projects. The upcoming Assembly database provides a description of sequences that make up each assembly and allows tracking of changes to an assembly. The NCBI Genome Remapping Service maps a set of annotations from one assembly to another via assembly-assembly alignments, and the Genome Decoration page takes user-generated genome annotation and creates a publication-quality graphic depicting the annotations distributed on the genome. The BioProject database provides access to the metadata about genome-wide research projects and links to the projects’ primary data that is deposited in archival databases. The equine research community has considerable interest in improving genome annotation with next generation sequencing datasets; the Transcriptome Shotgun Assembly (TSA) division of GenBank is the archive for computationally assembled sequences from ESTs, traces and next generation sequencing. TSA submissions can currently be considered for use in NCBI’s genome annotation pipeline to improve gene models; development to support the use of raw short read data for genome annotation is underway.