Rubus GDR RefTrans V2
Materials & Methods
GDR Rubus RefTrans V2 combines peer-reviewed published RNA-Seq and EST data sets to create a reference transcriptome (RefTrans, 24,264 sequences) for Rubus and provides putative gene function identified by homology to known proteins.
In Rubus RefTrans V2, 265 million Illumina paired-reads from publicly available peer-reviewed Rubus RNA-Seq data set (Hyun et al. 2014 [SRR975478], Hyun et al. 2014 [SRX347804], Garcia-Seco et al. 2015 [PRJEB6680] ) and 6,568 ESTs, were downloaded from the NCBI Short Read Archive database, the EBI database and the NCBI dbEST database, respectively. The RNA-Seq reads and ESTs were assembled by using the Mainlab RefTrans pipeline (manuscript in preparation – details of pipeline provided ahead of publication on request). The RefTran sequences were functionally characterized by pairwise comparison using the BLASTX algorithm against the Swiss-Prot (UniProtKB/Swiss-Prot Release 2017_04) and TrEMBL (UniProtKB/TrEMBL Release 2017_04) protein databases. Information on the top 10 matches with an expectation (E) value of ≤ 1E-06 were recorded and stored in GDR together with the RefTrans sequences. InterPro domains and Gene Ontology assignments were made to Rubus RefTrans V1 using InterProScan at the EBI through Blast2GO. The transcriptome and associated annotation are available to download, search by name, keyword (functional description), or mapped location, and view on the genome through JBrowse.