Computational protocol: Klebsiella pneumoniae Multiresistance Plasmid pMET1: Similarity with the Yersinia pestis Plasmid pCRY and Integrative Conjugative Elements

Similar protocols

Protocol publication

[…] Growth of bacteria was in Lennox L broth (1% tryptone, 0.5% yeast extract, 0.5% NaCl). Plasmid DNA was prepared using the Qiagen plasmid mini kit (Qiagen, Inc.). Recombinant clones were sequenced using BigDye (ABI) and DYEnamic ET (Amersham) chemistries on an ABI Prism (model 310 or 3100) instrument and the appropriate commercial or custom-designed primers. The complete circular nucleotide sequence of pMET1 has been deposited in the GenBank sequence library and assigned the accession number EU383016. Sequences were examined and assembled with Sequencher 4.7 software (Gene Codes Corp.). DNA and protein sequence analyses were performed using the CLUSTAL W program (Pôle Bio-Informatique Lyonnais server [http://pbil.ibcp.fr/cgi-bin/npsa_automat.plpagenpsa_clustalw.html]) , the Promoter prediction code (http://www.fruitfly.org/seq_tools/promoter.html) , the Basic local alignment search tool (BLAST) (http://www.ncbi.nlm.nih.gov/BLAST/) , and Artemis (http://www.sanger.ac.uk/Software/Artemis/). The sequence logo was generated using the Weblogo web based application (http://weblogo.berkeley.edu/) , . […]

Pipeline specifications

Software tools Sequencher, Clustal W, BLASTN, WebLogo
Application Genome data visualization
Organisms Yersinia pestis, Klebsiella pneumoniae, Escherichia coli
Diseases Liver Abscess, Pneumonia