Computational protocol: Genetic diversity of Plasmodium vivax population before elimination of malaria in Hainan Province, China

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Protocol publication

[…] The nested PCR products of pvmsp-1, pvcsp were directly sequenced in both directions using an ABI PRISM3730 DNA sequencer by Sangon Biotech (Shanghai, China). Nucleotide or amino acid sequences obtained from the blood samples of the malaria patients in this study were compared by CLUSTAL X and BioEdit 5.0 programme with the following published sequences: VK210 (accession no. M28746) and VK247 (accession no. M28745) of pvcsp and Sal-I (accession no. M75674) and Belem (accession no. M60807) of pvmsp-1, respectively. Sequence relationship trees of the pvmsp-1 and pvcsp genes from the Hainan isolates and published sequences from isolates of different geographic locations of world were constructed using neighbour-joining method implemented in MEGA 3 program []. Bootstrap proportions were used to assess the robustness of the tree with 1,000 bootstrap replications. […]

Pipeline specifications

Software tools Clustal W, BioEdit, MEGA
Application Phylogenetics
Organisms Plasmodium vivax
Diseases Goiter, Endemic, Malaria, Malaria, Falciparum