Automated RNA gene annotation

Most gene sets that are imported into Ensembl Metazoa do not have RNA gene annotation, and in these cases we perform automated annotation. For release 36 of Ensembl Metazoa RNA genes were annotated on all species except those imported from FlyBase, VectorBase, and WormBase. The RNA gene annotation uses three sources:

• miRBase provide genomic locations of precursor microRNA genes for a subset of species (Apis mellifera, Heliconius melpomene, Nasonia vitripennis, Strongylocentrotus purpuratus).
• tRNAscan-SE is used to predict tRNA genes (with a score threshold of 65).
• Rfam covariance model alignments are used to annotate RNA genes of all classes except tRNA. Models are restricted to those that are taxonomically appropriate, and are filtered to prevent overlapping genes (on either strand).

RNA genes have been updated for 26 species (21 of which had out-dated RNA gene annotation from earlier Ensembl Metazoa releases, the remaining 5 having partial annotation from the geneset provider); and added to 11 species which previously had no RNA gene annotation.

The chart below shows the numbers of RNA genes annotated, broken down by biotype, across all 37 species (click image for a larger version).

Funding

Ensembl Metazoa recieves funding from the Infravec2, to serve as a data delivery mechanism for that project. Infravec2 is an international and interdisciplinary research project on insect vectors of human and animal disease, including mosquitoes, sandflies and other flies. Infravec2 is funded by the Horizon 2020 Research Infrastructure Program (INFRAIA) of the European Union under grant agreement No 731060.

Ensembl Genomes is developed by EMBL-EBI and is powered by Ensembl software system for the analysis and visualisation of genomic data. For details of our funding please click here.