Rubus GDR RefTrans V2

Analysis NameRubus GDR RefTrans V2
Methodreftrans (v2)
SourceRubus GDR RefTrans V2
Date performed2017-05-10

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-readfrom 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.




RefTrans in FASTA format  (24,264 sequences) Rubus  RefTrans v2 FASTA format 

Homology Analysis 

Homology was determined using the BLASTx algorithm with an e-value cutoff of 1.0 e-6 for the Rubus RefTrans V2 vs. the Swiss-Prot (UniProtKB/Swiss-Prot Release 2017_04), TrEMBL(UniProtKB/TrEMBL Release 2017_04).  Only the best match was kept. 


BLAST of refTrans to Swiss-Prot EXCEL format (72% refTrans with homologies) Rubus  RefTrans V2 vs Swissprot
RefTrans with homologies  FASTA format Rubus RefTrans V2 vs Swissprot_hit
RefTrans without homologies FASTA format Rubus  RefTrans V2 vs Swissprot_noHit


BLAST of refTrans to TrEMBL EXCEL format (90% refTrans with homologies) Rubus   RefTrans V2 vs TrEMBL
RefTrans with homologies  FASTA format Rubus  RefTrans V2 vs TrEMBL_hit
RefTrans without homologies FASTA format Rubus RefTrans V2 vs TrEMBL_noHit


InterProscan Analysis

InterPro domains and Gene Ontology assignments were made to Rubus  RefTrans V2 using InterProScan at the EBI through Blast2GO.
Gene Ontology annotations by RefTrans EXCEL format  Rubus  RefTrans V2 Gene Ontology annotations
InterPro annotations by RefTrans EXCEL format Rubus  RefTrans V2 InterPro annotations


KEGG Analysis

KEGG pathway and ortholog assignments were made to Rubus  RefTrans V2 using the KEGG / KASS server at 
KEGG pathway annotations by RefTrans EXCEL format Rubus  RefTrans V2 KEGG pathways
KEGG ortholog annotations by RefTrans EXCEL format Rubus  RefTrans V2 KEGG orthologs



The alignment tool 'BLAT' was used to map Rubus  RefTrans V2 to the Rubus occidentalis genome v1.0.a1 Alignments with an alignment length of 95% and 90% identify were preserved. 
BLAT of refTrans to Rubus occidentalis genome v1.0.a1 EXCEL format Rubus  RefTrans V2_Rubus occidentalis genome v1.0.a1