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Pipeline publication

[…] The loss of a small tRNASec binding domain at the protein N terminus was identified as the hallmark of SelA homologs with a function different from selenocysteinyl-tRNASec biosynthesis., The species tree was based on a rooted maximum-likelihood phylogeny of 454 phylum level phylogenetic markers for ε-proteobacteria (). The tree was processed in the R software environment using functions of the Ape library (). Tips were purged to include the genomes selected for the analysis with the “drop.tip” function, and the resulting tree was rendered ultrametric with the “chronos” function. Traits of gene presence/absence were plotted alongside the tips (see ) using the “table.phylo4d” function of the Adephylo package (). The phylogenetic tree of SelA proteins was obtained using the maximum-likelihood method implemented in the RaxML program ver. 7.7.8 () using the PROTCATGTR amino acid substitution model. The SelA tree was compared with the species tree using the Ape “cophyplot” function. The prokaryotic SelA tree (see ) was rendered using Figtree ( , Complete prokaryotic genomes were downloaded from the NCBI (National Center for Biotechnology Information) ftp site; ε-proteobacteria genomes considered for the analysis were selected from genome report files based on the availability of whole-genome phylogeny () and clustered using a Genomic Similarity Score (GSSa) = 0.95 (). Proteins of the Sel machinery were identified by homology using annotated sequences from Campylobacter jejuni. Bona fide MnmH and YedF proteins from Sulfurimonas autotrophica and Campylobacter lari, encoded in Sel operons, were used as reference sequences to search proteins involved in selenium metabolism. Searche […]

Pipeline specifications

Software tools adephylo, RAxML, FigTree
Organisms Helicobacter pylori, Homo sapiens, Helicobacter acinonychis
Diseases Stomach Diseases, Gastrointestinal Neoplasms, Digestive System Neoplasms
Chemicals Selenium, Chalcogens, Selenocysteine, Amino Acids, Sulfur