Computational protocol: Genetic diversity and stability of the porA allele as a genetic marker in human Campylobacter infection

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Protocol publication

[…] Codon-aligned porA nucleotide and amino acid sequences were constructed using the program Seqlab in gcg (Wisconsin Package version 10.3, Accelerys) to identify conserved and variable regions of the allele. Sites in the sequence alignment at which positive immune selection had occurred were detected by use of snap.pl (; ), available at http://www.hiv.lanl.gov. This program calculates synonymous (dS) and non-synonymous (dN) substitution rates by the method of and incorporates a statistic developed by . Sites of positive immune selection were defined as those at which a greater number of non-synonymous to synonymous substitutions were identified.The association between clonal complex and porA allele was measured using a permutation test in which actual data and 1000 random associations were compared.Phylogenetic relationships among porA alleles were determined using ClonalFrame (). Sequence data from alleles were aligned using the program muscle, available at http://www.ebi.ac.uk/Tools/muscle/index.html, to obtain an input file for ClonalFrame. A 75 % consensus tree was constructed from five convergent replicate trees, by setting both the number of burn-in iterations and the number of Monte Carlo Markov chain (MCMC) iterations to 50 000. Convergence of the MCMC between replicates was determined by a statistic below 1.2 for each parameter. […]

Pipeline specifications

Software tools ClonalFrame, MUSCLE
Applications Phylogenetics, Nucleotide sequence alignment
Organisms Campylobacter jejuni, Campylobacter coli, Homo sapiens
Diseases Infection
Chemicals Nucleotides