Computational protocol: Signal transduction-related responses to phytohormones and environmental challenges in sugarcane

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Protocol publication

[…] Sugarcane sequences containing a putative pkinase (catalytic domain of protein kinases) domain, as defined by the Pfam algorithm [] were selected for the phylogenetic analysis of RLKs and other protein kinases. Protein kinase sequences from other organisms were retrieved in their majority from the PlantsP database [] and used as drivers in the phylogenetic analysis. The sequences were aligned using ClustalW [] with default parameters. The pkinase alignment was manually adjusted to preserve the conserved subdomains defined by Hanks and colleagues [-] for eukaryotic kinases using the Se-Al Sequence Alignment Editor []. The alignment was trimmed to remove gaps in most of the sequences. Sequences spanning less than 50% of this partial alignment were discarded. The alignment was analysed with PAUP [] using the neighbor-joining (NJ) algorithm and distance as the criterion. Bootstrap analysis was conducted with 500 replicates using NJ/UPGMA and distance as the criterion. […]

Pipeline specifications

Software tools Clustal W, Se-Al, PAUP*
Databases Pfam PlantsP
Applications Phylogenetics, Nucleotide sequence alignment
Chemicals Abscisic Acid, Carbon, Sucrose