Computational protocol: Evidence for horizontal gene transfer between Chlamydophila pneumoniae and Chlamydia phage

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Protocol publication

[…] All sequence data were gathered from the NCBI's GenBank database (May 2014) (http://www.ncbi.nlm.nih.gov/genbank/; see ). Orthologs were identified using the Basic Local Alignment Search Tool (BLAST; ref. 29) at NCBI. For BLASTN, sequences were considered to be homologous if the expect- (e-) value was <1 × 10−5. For BLASTP, sequences were considered to be homologous if the e-value was <1 × 10−20. Multiple sequence alignments were performed with Multiple Sequence Comparison by Log-Expectation (MUSCLE) algorithm (http://www.ebi.ac.uk/Tools/msa/muscle/; ref. 30). Phylogenies were constructed using Molecular Evolution Genetic Analysis, version 5.2.2 (MEGA 5; ref. 31). The best substitution models for both DNA and protein phylogenies were determined by calculation of the BIC statistic as described in the appropriate figure legends. Additionally, all trees were constructed using the maximum-likelihood tree building method with bootstrapping of 1000 iterations.Comparison of synteny in regions where PRIP genes are found in the different bacterial strains was performed using the web-based version of the Artemis Comparison Tool, WebACT. […]

Pipeline specifications

Software tools BLASTN, BLASTP, MUSCLE, MEGA, ACT, WebACT
Applications Phylogenetics, Nucleotide sequence alignment, Genome data visualization
Organisms Escherichia coli, Chlamydia pneumoniae, Phascolarctos cinereus
Diseases Chlamydia Infections, Nematode Infections, Chlamydial Pneumonia