Computational protocol: Comparative genomic analysis of Acinetobacter spp. plasmids originating from clinical settings and environmental habitats

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Protocol publication

[…] DNA samples obtained after ultracentrifugation were separately sequenced using MiSeq Illumina technology at the Center for Biotechnology (CeBiTec) in Bielefeld, Germany. The reads obtained were assembled using GS de novo Assembler software (gs Assembler, version 2.8, Roche). Plasmid finishing was accomplished using the CONSED software package. Complete closed replicons were automatically annotated by the genome annotation system GenDB and manually curated. Genes were annotated using the best BLASTP hit at the National Center for Biotechnology Information (NCBI) database ( Replicon sequences were submitted to GenBank and registered under Bioproject ID PRJEB22129.Sequence alignment and graphic comparison were performed using the genome comparison visualizer Easyfig. [...] Protein alignments were carried out using ClustalW default parameters. Plasmids were classified according to their relaxase proteins as described by Garcillán-Barcia et al.. MOB families and subfamilies were also defined as in Garcillán-Barcia et al.. MOB relaxase and Rep_3 family phylogenetic analysis was carried out by maximun likelihood (ML) using PhyML 20131016. The best evolutionary model for each multiple alignment was established by ProtTets 2.4. Bootstrap values of 100 were chosen for ML analysis. Rep_3 database sequences used for phylogenetic tree calculation are listed in Table . […]

Pipeline specifications

Software tools Newbler, Consed, GenDB, BLASTP, Easyfig, Clustal W, PhyML
Applications Phylogenetics, Genome data visualization
Diseases Acinetobacter Infections