Computational protocol: A third mitochondrial RNA polymerase in the moss Physcomitrella patens

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Protocol publication

[…] Sequence information was retrieved from the National Center for Biotechnology Information (http://www.ncbi.nlm.nih.gov/BLAST) employing the BLASTP and TBLASTN algorithms and from the Joint Genome Institute (http://genome.jgi-psf.org/). For translation and alignment, sequences were subsequently imported into GENEIOUS (Drummond et al. ). Multiple protein sequence alignments were generated using CLUSTALW (Thompson et al. ) implemented in the GENEIOUS package. The phylogeny was reconstructed by the PhyML algorithm V3.0 (Guindon et al. ) with 100 bootstrap replicates. The aligned sequence data comprised 894 amino acids lacking only the less conserved N-terminal portion of the proteins. For the reconstruction, the LG amino acid replacement model was employed. A discrete gamma distribution with four categories was assumed to approximate the continuous function (shape: 1,004/inv: 0,138). Essentially, the same tree topology was obtained employing Bayesian (Ronquist and Huelsenbeck ) and neighbor joining analysis (Saitou and Nei ). The tree was rooted with the four green algae RPOT proteins indicated. Tree reconstruction was based on a multiple alignment of 54 plant RPOT sequences (Supplementary Table 2). […]

Pipeline specifications

Software tools BLASTP, TBLASTN, Geneious, Clustal W, PhyML
Applications Phylogenetics, Amino acid sequence alignment
Organisms Physcomitrella patens, Arabidopsis thaliana