Computational protocol: Identification and characterisation of tomato torrado virus, a new plant picorna-like virus from tomato

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Protocol publication

[…] Cloned cDNA fragments and PCR products were sequenced directly. Sequence analysis was performed using an Applied Biosystems 3100 Genetic Analyser, with a DYEnamic ET Terminator Cycle Sequencing Kit (Amersham) and the primers that had been used for amplification. For additional PCR fragments, ToTV-specific primers were used for primer-walking sequencing.Nucleotide and amino acid sequence data were analyzed and assembled using the DNASTAR package (Lasergene). Blast searches were carried out using the NCBI Blast server ( with all available databases. Sequence comparisons with other viruses were performed with programs from the PHYLIP package. Multiple alignments and phylogenies were performed with the CLUSTAL X program after bootstrapping in 1000 replicates. Neighborjoining consensus phylogenies were viewed by the NJplot program [] and printed using TreeView []. […]

Pipeline specifications

Software tools BLASTN, PHYLIP, Clustal W, NJplot, TreeViewX
Application Phylogenetics
Organisms Solanum lycopersicum, Tomato torrado virus
Diseases HIV Infections