P. sativum CSFL RefTrans V2

Overview
Analysis NameP. sativum CSFL RefTrans V2
Methodreftrans (2.0)
Sourcep.sativum_csfl_reftransV2
Date performed2017-09-19

Materials & Methods

CSFL Pisum sativum RefTrans V2 combines peer-reviewed published RNA-Seq and EST data sets to create a reference transcriptome (RefTrans, 63,990 sequences) for Pisum sativum and provides putative gene function identified by homology to known proteins.

In Pisum sativum RefTrans V2, 2.4 billion RNA-Seq reads from publicly available, peer-reviewed Pisum sativum RNA-Seq data sets (Trujillo et al. 2014 [SRP045233]Sudheesh et al. 2015 [SRP056009,SRP056105]Yendrek et al. 2015 [SRP009826], Susete Alves-Carvalho et al. 2015 [SRP049810], Liu N et al. 2015 [SRP063052], Zhukov VA et al. 2015[SRP058689], Kerr et al. 2017 [SRP068822]and 18,576 ESTs, were downloaded from the NCBI Short Read Archive 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_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 Pisum sativum 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  (63,990 sequences) Pisum sativum 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 Pisum sativum RefTrans V2 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 (73% refTrans with homologies) Pisum sativum RefTrans V2 vs Swissprot
RefTrans with homologies  FASTA format Pisum sativum RefTrans V2 vs Swissprot_hit
RefTrans without homologies FASTA format Pisum sativum RefTrans V2 vs Swissprot_noHit

UniProtKB/TrEMBL

BLAST of refTrans to TrEMBL EXCEL format (93% refTrans with homologies) Pisum sativum RefTrans V2 vs TrEMBL
RefTrans with homologies  FASTA format Pisum sativum RefTrans V2 vs TrEMBL_hit
RefTrans without homologies FASTA format Pisum sativum RefTrans V2 vs TrEMBL_noHit

 

InterProscan Analysis

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

 

KEGG Analysis

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