Computational protocol: Trypanosoma vivax is the second leading cause of camel trypanosomosis in Sudan after Trypanosoma evansi

Similar protocols

Protocol publication

[…] The ITS region of T. evansi (ITS1 + 5.8S + ITS2 rDNA, ~1100 bp) and the TviCatL-PCR sequences (~200 bp) of T. vivax were each edited manually to correct possible base calling errors using the BioEdit 7.0 software program [] and were subsequently joined to reconstruct a 950 bp fragment of the ITS gene and a 160 bp fragment of the TviCatL gene. The consensus sequences were aligned with sequences that were publicly available in the GenBank database using the Clustal X 2.1 software program [].Phylogenetic trees were constructed using the neighbour-joining method implemented in the Mega software program (version 6.0) []. The best substitution models, as determined by the model test algorithm [] implemented in the Mega software program were T92 + G and K2 + I for ITS-T. evansi. All sequences generated in this study were deposited in the GenBank database under the accession numbers (LC199490, LC199491, LC198227, LC198229–LC198233). [...] A chi-squared test to investigate the differences in the prevalence of trypanosome infections in the two study areas was performed using the GraphPad Prism software program (GraphPad Software Inc., CA, USA). Cohen’s kappa coefficient was calculated using VassarStats: Website for Statistical Computation (http://www.vassarstats.net/kappa.html); the results were interpreted according to a previously described method []. The associations between the hematocrit values in the infected and non-infected animals (with each of the trypanosomes), as determined by different diagnostic tests, were analysed using Student's t-test. P-values were determined using the GraphPad Prism software program (GraphPad Software Inc., CA, USA). P-values of < 0.05 were considered to indicate statistical significance. […]

Pipeline specifications

Software tools BioEdit, Clustal W, MEGA, VassarStats
Applications Miscellaneous, Phylogenetics
Organisms Camelus dromedarius
Diseases Coinfection