Computational protocol: Functional characterization of ent copalyl diphosphate synthase, kaurene synthase and kaurene oxidase in the Salvia miltiorrhiza gibberellin biosynthetic pathway

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Protocol publication

[…] The SmCPSent, SmKS and SmKO sequences were confirmed at NCBI (http://www.ncbi.nlm.nih.gov/). The open reading frames (ORFs) and deduced amino acid sequences were analyzed using the online tool ORF Finder (http://www.ncbi.nlm.nih.gov/gorf/gorf.html) and the ExPASy online tool (http://web.expasy.org/translate/), respectively. The ChloroP 1.1 Server (http://www.cbs.dtu.dk/services/ChloroP/) was used to predict chloroplast transit peptides. The sequences of the SmCPSent, SmKS and SmKO as well as other corresponding sequences downloaded from GenBank were aligned using the DNAMAN program, and the phylogenetic trees for SmCPSent, SmKS and SmKO were constructed using sequences from other plants () using the neighbor-joining method in MEGA5.1 . […]

Pipeline specifications

Software tools Open Reading Frame Finder, ChloroP, DNAMAN, MEGA
Databases ExPASy
Organisms Saccharomyces cerevisiae, Salvia miltiorrhiza