Computational protocol: Conserved Function of Core Clock Proteins in the Gymnosperm Norway Spruce (Picea abies L. Karst)

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Protocol publication

[…] Putative spruce circadian clock homologs were identified through tblastn searches against the spruceEST database at PlantGDB (http://www.plantgdb.org/) using Arabidopsis genes as queries. Full-length genes were obtained by rapid amplification of cDNA ends (Gyllenstrand et al. unpublished). Predicted amino acid sequences of putative spruce clock genes and homologous Arabidopsis genes were aligned using Clustal W . Phylogenetic reconstructions were done using PhyML 3.0 and visualized using FigTree 1.2.3 (http://tree.bio.ed.ac.uk/software/figtree/). A Blast search using PaGI as query resulted in only one significant hit in the Arabidopsis genome (at1g22770, GIGANTEA, e-value 0.0), which was thus considered as the closest homolog. […]

Pipeline specifications

Software tools TBLASTN, Clustal W, PhyML, FigTree
Databases PlantGDB
Applications Phylogenetics, Amino acid sequence alignment
Organisms Arabidopsis thaliana, Picea abies, Pseudomonas phage PRR1