Computational protocol: Regulation of the cholesterol biosynthetic pathway and its integration with fatty acid biosynthesis in the oleaginous microalga Nannochloropsis oceanica

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Protocol publication

[…] The Arabidopsis protein sequences were retrieved from http://www.arabidopsis.org/. Microalgal genomes were retrieved from the links in Additional file : Table S2. Proteins from all genomes were blasted with the Arabidopsis protein queries (Additional file : Table S1) using the standalone BLAST software package. The Conserved Domain Database (http://www.ncbi.nlm.nih.gov/cdd/), Pfam (http://pfam.sanger.ac.uk/search), and SMART [] plus previous genome annotations were employed to confirm the accuracy of chosen sequences. If more than one allele existed, the best-match allele was chosen as representative for the similarity heatmap analysis. The sequences ultimately selected are listed in Additional file . Gaps and ambiguously aligned sites were removed using CLUSTALW [], gBlock [], and manual validation. ProtTest [] and PhyML 3.0 [] were used to select the available model of protein substitution and phylogenetic analyses with a maximum likelihood method. Bootstrap support values were estimated using 100 pseudo-replicates. […]

Pipeline specifications

Software tools Clustal W, Gblocks, ProtTest, PhyML
Databases Pfam CDD
Application Phylogenetics
Organisms Nannochloropsis oceanica
Chemicals Cholesterol, Nitrogen, Phytosterols, Squalene, Sterols