Computational protocol: Functional characterization of the diatom cyclin-dependent kinase A2 as a mitotic regulator reveals plant-like properties in a non-green lineage

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Protocol publication

[…] Sequence data was retrieved from the NCBI RefSeq database (A. thaliana, C. merolae, C. reinhardtii, D. melanogaster, H. sapiens, N. gaditana, P. sojae, S. cerevisiae, S. pombe and X. laevis), through the JGI portal (P. tricornutum and T. pseuodonana) or the pico-PLAZA database (E. siliculosus, F. cylindrus, M. pusilla, M. sp., O. tauri and O. lucimarinus) [,]. Multiple alignments based on CDK amino acid sequences were generated with MUSCLE [] and then manually improved, yielding 226 amino acid positions (Additional file : Figure S3). To define subclasses within the gene families, phylogenetic trees were built that included reference CDK sequences from animals, yeast, higher plants, stramenopiles and several algal species. MEGA5.1 was used to construct the maximum-likelihood tree using the rtREV + G + I model. To test the significance of the nodes, bootstrap analysis was applied using 1,000 replicates. […]

Pipeline specifications

Software tools MUSCLE, MEGA
Databases pico-PLAZA
Applications Phylogenetics, Nucleotide sequence alignment
Organisms Phaeodactylum tricornutum