V. faba CSFL RefTrans V2

Overview
Analysis NameV. faba CSFL RefTrans V2
Methodreftrans (v2)
Sourcev.faba_csfl_reftransV2
Date performed2017-09-12

Materials & Methods

CSFL Vicia faba RefTrans V2 combines peer-reviewed published RNA-Seq and EST data sets to create a reference transcriptome (RefTrans, 37,378 sequences) for Vicia faba and provides putative gene function identified by homology to known proteins.

In Vicia faba RefTrans V2, 616 million RNA-Seq reads from publicly available, peer-reviewed faba bean RNA-Seq data sets (Suresh et al. 2013 [SRP043650],  Ray et al.  2015 [SRP038935], Webb et al. 2015 [SRP033593,SRP033121], Zhang et al. 2015 [ERP009949], Ocaña S et al. 2015 [SRP045955], Arun-Chinnappa and McCurdy. 2015 [SRP055969], Macas et al, 2015 [ERP004630], Cooper et al, 2017 [SRP098697] ), and 20,697 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 using the Mainlab RefTrans pipeline (manuscript in preparation – details of pipeline provided ahead of publication on request). The RefTrans sequences were functionally characterized by pairwise comparison using the BLASTX algorithm against the Swiss-Prot (UniProtKB/Swiss-Prot Release 2017_06) and TrEMBL (UniProtKB/TrEMBL Release 2017_06) protein databases.  Information on the top 10 matches with an expectation (E) value of ≤ 1E-06 were recorded and stored in CSFL together with the RefTrans sequences. InterPro domains and Gene Ontology assignments were made to Vicia faba RefTrans V2 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.

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Assembly

 
RefTrans in FASTA format  (37,378 sequences) Vicia faba  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 Vicia faba RefTrans V2 vs. the Swiss-Prot (UniProtKB/Swiss-Prot Release 2017_06), TrEMBL(UniProtKB/TrEMBL Release 2017_06).  Only the best match was kept. 

UniProtKB/Swiss-Prot

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

UniProtKB/TrEMBL

BLAST of refTrans to TrEMBL EXCEL format (92% refTrans with homologies) Vicia faba   RefTrans V2 vs TrEMBL
RefTrans with homologies  FASTA format Vicia faba  RefTrans V2 vs TrEMBL_hit
RefTrans without homologies FASTA format Vicia faba RefTrans V2 vs TrEMBL_noHit

 

InterProscan Analysis

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

 

KEGG Analysis

KEGG pathway and ortholog assignments were made to Vicia faba  RefTrans V2 using the KEGG / KASS server at http://www.genome.jp/kaas-bin/kaas_main. 
KEGG pathway annotations by RefTrans EXCEL format Vicia faba  RefTrans V2 KEGG pathways
KEGG ortholog annotations by RefTrans EXCEL format Vicia faba  RefTrans V2 KEGG orthologs