Computational protocol: Lipids containing medium-chain fatty acids are specific to post-whole genome duplication Saccharomycotina yeasts

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Protocol publication

[…] Lysophospholipid acyltransferase (LPLAT) gene family members were extracted from various databases (NCBI, Génolevures) using the Blastp program or from Scannel et al. []. S. cerevisiae protein sequences from the Saccharomyces Genome Database (SGD) were used as bait (Additional file : Table S2). Geotrichum candidum gene sequences were obtained from the complete genome sequence (Morel et al., in preparation). Sequence alignments were generated using MUSCLE ver. 3.7 implemented in phylogeny.fr, using default parameters [] or MAFFT ver. 7 (http://mafft.cbrc.jp/alignment/server/), using blosom62 matrix and default parameters and were manually adjusted with GeneDoc (http://www.nrbsc.org/gfx/genedoc/). Phylogenetic trees were reconstructed with the PhyML program implemented in phylogeny.fr, using default parameters [] or the Maximum Likelihood program [] implemented in MEGA6 []. Phylogenetic trees were visualized using NJPlot []. Multiple Sequence Alignment raw data were available in Additional files and . […]

Pipeline specifications

Software tools BLASTP, Phylogeny.fr, MAFFT, PhyML, MEGA, NJplot
Databases SGD Genolevures
Application Phylogenetics
Organisms Saccharomyces cerevisiae
Chemicals Fatty Acids