Rubus occidentalis Whole Genome v3.0 Assembly & Annotation
VanBuren,R., Wai,C.M., Colle,M., Wang,J., Sullivan,S., Bushakra,J.M., Liachko,I., Vining,K.J., Dossett,M., Finn,C.E., et al. (2018) A near complete, chromosome-scale assembly of the black raspberry (Rubus occidentalis) genome. GigaScience, 7. (GDR | Journal)
The Rubus occidentalis v3.0 gene prediction files are available in FASTA and GFF3 formats.
All annotation files are available for download by selecting the desired data type in the left-hand "Resources" side bar. Each data type page will provide a description of the available files and links do download. Alternatively, you can use the FTP repository for bulk download.
Homology of the Rubus occidentalis v3.0 protein was determined by pairwise sequence comparison using the blastp algorithm against various protein databases. An expectation value cutoff less than 1e-9 was used for the NCBI nr (Release 2017-07) and 1e-6 for the Arabidoposis proteins (TAIR10), UniProtKB/SwissProt (Release 2018-04), and UniProtKB/TrEMBL (Release 2018-04) databases. The best hit reports are available for download in Excel format.
Functional annotation for the Rubus occidentalis v3.0 genome are available for download below. The Rubus occidentalis proteins were analyzed using InterProScan in order to assign InterPro domains and Gene Ontology (GO) terms. Pathways analysis was performed using the KEGG Automatic Annotation Server (KAAS).