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 (www.ncbi.nlm.nih.gov) 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