Computational protocol: The qacC Gene Has Recently Spread between Rolling Circle Plasmids of Staphylococcus, Indicative of a Novel Gene Transfer Mechanism

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Protocol publication

[…] All plasmid sequences used in this study were downloaded from GenBank. Sequence similarity searches were performed by BlastP and BlastN at NCBI. Multiple alignments were produced by Clustal W or Muscle. Circular homology plots were based on sequence alignments with gaps >12 nucleotides removed before calculating the percentage homology using a window of 30 nucleotides. DNA structural properties were assessed as previously described in Pedersen et al. (). […]

Pipeline specifications

Software tools BLASTP, BLASTN, Clustal W, MUSCLE
Application Nucleotide sequence alignment
Chemicals Lincomycin, Nucleotides, Ammonium Compounds