Computational protocol: Assessment of Plasmodium falciparum resistance to ferroquine (SSR97193) in field isolates and in W2 strain under pressure

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Protocol publication

[…] In order to obtain a more accurate phylogeny of the PfCRT protein, a Bayesian phylogenetic analysis of PfCRT sequences was performed. For 3D7, Dd2 and HB3 clones, sequences were obtained from databanks (GenBank accession numbers: 3D7: CAD50842; Dd2: AAF26926; HB3: AAF60275). PfCRT sequences from field isolates were reported previously []. In total, 37 full-length PfCRT amino acid sequences were aligned using the BioEdit v7.0.1 package []. Alignment was facilitated by the fact that i) PfCRT protein sequences were extremely conserved (96–98% identity) and ii) none of these sequences exhibited any gaps or insertions, yielding 427 sites for analysis. The alignment used in this study is available upon request to the corresponding author. Phylogenetic analysis of this protein data set was carried out using software "MrBAYES", version 3_0b4 []. Bayesian analysis was performed using the Jones-Taylor-Thornton (JTT) amino acid replacement model []. Starting trees were random, four simultaneous Markov chains were run for 100,000 generations, burn-in values were set at 15,000 generations (based on empirical values of stabilizing likehoods), and trees were sampled every 100 generations. Bayesian posterior probabilities were calculated using a Markov chain Monte Carlo (MCMC) sampling approach implemented in MrBAYES 3_0b4 []. […]

Pipeline specifications

Software tools BioEdit, MrBayes
Application Phylogenetics
Organisms Plasmodium falciparum, Homo sapiens
Diseases Malaria, Malaria, Falciparum
Chemicals Chloroquine