Computational protocol: Re evaluation of the species of hookworms infecting dogs in Central Vietnam

Similar protocols

Protocol publication

[…] For adult worms and COX-1 PCRs, products were purified by Exonuclease I (ExoI) and FastAPTM Thermosensitive Alkaline Phosphatase and submitted for bidirectional DNA sequencing at The Melbourne Translational Genomics Platform (The University of Melbourne) or Macrogen Inc (Korea).DNA sequences resulting from a 377-base pair fragment of the COX1 gene were read with Finch TV version 1.4.0 trace viewer (Geospiza, Inc., Seattle, WA, USA) and aligned with BioEdit version 7.2.3 (www.mbio.ncsu.edu/BioEdit/bioedit.html) using COX-1 gene sequences from the following hookworm species: A. ceylanicum Malaysia isolates (GenBank no. KC247727– KC247745, Human Sg Bumbun 19, Human Pos Iskandar 11; Cambodian Isolates (Genbank no. KF896596–KF896605), Southern China isolates (KP072074 and KP072071), A. caninum (NC012309) and A. duodenale (NC003415.1). Neighbor-joining analyses were conducted by using Tamura-Nei parameter distance estimates on a 257 base pair region of aligned sequences. Bootstrap analyses were conducted using 1,000 replicates and the tree was constructed by using Mega 6 (http://www.megasoftware.net/) []. [...] The data were analysed using IBM SPSS Statistics v21 (SPSS Inc., Chicago, IL, USA). The prevalence of hookworm infection was calculated by using descriptive statistics. […]

Pipeline specifications

Software tools BioEdit, MEGA, SPSS
Applications Miscellaneous, Phylogenetics
Organisms Canis lupus familiaris, Dipturus trachyderma, Homo sapiens
Diseases Coinfection