Computational protocol: Effect of temperature on the pathogenesis, accumulation of viral and satellite RNAs and on plant proteome in peanut stunt virus and satellite RNA-infected plants

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Protocol publication

[…] Since annotation of many identified proteins and ESTs turned out to be incomplete we performed an array of complementary analyses to determine their functions. First, we applied Blast2GO software (Conesa and Götz, ) to associate GO terms with Mascot hits. This tool utilizes information on top BLAST hits (we performed local BLASTp or BLASTx search with e-value cut-off of 1e-25 against set of all protein sequences of Solanaceae and Arabidopsis thaliana from RefSeq database) and predicted protein domains to annotate the query. Additionally we used KAAS (KEGG Automatic Annotation Server, Moriya et al., ) to acquire KEGG annotations. This tool classifies each sequence to an orthologous cluster and retrieves annotations assigned to it. Finally, we performed direct BLAST (Altschul et al., ) search against the tomato proteome (Solanum lycopersicum, up000004994) and manually gathered annotation from publicly available databases in order to compare identified proteins with sequences from well-annotated relatives. All obtained information were carefully curated and compared. KAAS identifications were used to project expression data onto KEGG metabolic networks of Tomato using CyKEGGParser (Cytoscape plugin developed by Nersisyan et al., ). […]

Pipeline specifications

Software tools Blast2GO, BLASTP, BLASTX, KAAS, CyKEGGParser
Databases KEGG
Application Protein interaction analysis
Organisms Peanut stunt virus
Diseases Infection