Vaccinium corymbosum GDV RefTrans V1

Overview
Analysis NameVaccinium corymbosum GDV RefTrans V1
Methodreftrans (1.0)
SourceVaccinium corymbosum GDV RefTrans V1
Date performed2017-05-03

Materials & Methods

GDV Vaccinium corymbosum RefTrans V1 combines peer-reviewed published RNA-Seq and EST data sets to create a reference transcriptome (RefTrans, 39,461 sequences) for Vaccinium corymbosum and provides putative gene function identified by homology to known proteins.

In  Vaccinium corymbosum RefTrans V1,  757 million readfrom publicly available peer-reviewed Vaccinium corymbosum RNA-Seq data set (Gupta et al. 2015 [SRP039977, SRP039971]LiL et al. 2016 [SRP091871] ) and 22,402 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 GDV together with the RefTrans sequences. InterPro domains and Gene Ontology assignments were made to Vaccinium corymbosum 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.

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Assembly

 
RefTrans in FASTA format  (39,461 sequences) Vaccinium corymbosum  RefTrans V1 FASTA format 

 

Homology Analysis 

Homology was determined using the BLASTx algorithm with an e-value cutoff of 1.0 e-6 for the Vaccinium corymbosum RefTrans v1 vs. the Swiss-Prot (UniProtKB/Swiss-Prot Release 2017_04), TrEMBL(UniProtKB/TrEMBL Release 2017_04).  Only the best match was kept. 

UniProtKB/Swiss-Prot

BLAST of refTrans to Swiss-Prot EXCEL format (68% refTrans with homologies) Vaccinium corymbosum  RefTrans V1 vs Swissprot
RefTrans with homologies  FASTA format Vaccinium corymbosum RefTrans V1 vs Swissprot_hit
RefTrans without homologies FASTA format Vaccinium corymbosum  RefTrans V1 vs Swissprot_noHit

UniProtKB/TrEMBL

BLAST of refTrans to TrEMBL EXCEL format (86% refTrans with homologies) Vaccinium corymbosum   RefTrans V1 vs TrEMBL
RefTrans with homologies  FASTA format Vaccinium corymbosum  RefTrans V1 vs TrEMBL_hit
RefTrans without homologies FASTA format Vaccinium corymbosum RefTrans V1 vs TrEMBL_noHit

 

InterProscan Analysis

InterPro domains and Gene Ontology assignments were made to Vaccinium corymbosum  RefTrans V1 using InterProScan at the EBI through Blast2GO.
Gene Ontology annotations by RefTrans EXCEL format  Vaccinium corymbosum  RefTrans V1 Gene Ontology annotations
InterPro annotations by RefTrans EXCEL format Vaccinium corymbosum  RefTrans V1 InterPro annotations

 

KEGG Analysis

KEGG pathway and ortholog assignments were made to Vaccinium corymbosum  RefTrans V1 using the KEGG / KASS server at http://www.genome.jp/kaas-bin/kaas_main. 
KEGG pathway annotations by RefTrans EXCEL format Vaccinium corymbosum  RefTrans V1 KEGG pathways
KEGG ortholog annotations by RefTrans EXCEL format Vaccinium corymbosum  RefTrans V1 KEGG orthologs