Computational protocol: Niche specific amino acid features within the core genes of the genus Shewanella

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[…] Highly similar paralogous sequences have been removed from each of the twelve set of genome sequences, based on a comparison of the gene list against itself (with identity >=90%) using Blastclust program (www.ncbi.nlm.nih.gov/Web/Newsltr/Spring04/blastlab.html ). From the rest of the genes, core genes were detected through putative one-to-one orthologous gene identification, using BLASTP (>= 85% identity and 0% gap). This search identified a total of 121 orthologous groups that had all twelve species represented, which were used for further analysis. [...] All core genes from 12 Shewanella genomes were used for generating a neighbor joining tree. For each twelve species, the amino acid sequences of 121 core gene sets were concatenated in order to produce twelve continuous sequences of average length 34,746 amino acids. Multiple Alignments of these 12 sets of concatenated core amino acid sequences were performed using CLUSTALW (http://www.ebi.ac.uk/clustalw/). A Neighbor-joining Phylogenetic tree based on these concatenated core amino acid sequences from the Shewanella species of interest, was generated using MEGA 5 [].The bootstrap values are shown in the Phylogenetic tree. […]

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