Computational protocol: The Prevalence of Angiostrongylus cantonensis/mackerrasae Complex in Molluscs from the Sydney Region

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Protocol publication

[…] Sequencing of the ITS-1 PCRs were carried out as previously described, using the plasmid as template. This was carried out as a control to confirm successful cloning. The concentration of plasmid solutions was confirmed using a NanoDrop ND-1000 UV spectrophotometer. The plasmid solutions were diluted in accordance with the guidelines provided by the service provider (Macrogen Inc, Korea), where the sequencing of the plasmid inserts was carried out using the universal plasmid primers T3 and T7. Analysis of chromatograms returned by Macrogen Inc. was carried out using Chromas Lite software (http://technelysium.com.au). After viewing the chromatograms in Chromas Lite, the low quality ends of sequences and any residual vector sequence was removed from each sequence. The resulting quality controlled sequences were then assembled manually by alignment using ClustalW. Online BLASTN searches against the NCBI nucleotide database were carried out on each resulting contig, to confirm homology to Angiostrongylus spp. ITS-1 sequences. All ITS-1 contigs were compared to each other by ClustalW alignment to determine whether substantial differences existed between the ITS-1 DNA regions of A. mackerrasae and A. cantonensis. […]

Pipeline specifications

Software tools Chromas, Clustal W, BLASTN
Application Sanger sequencing
Organisms Angiostrongylus cantonensis, Caenorhabditis elegans, Rattus norvegicus, Homo sapiens, Canis lupus familiaris, Helix aspersa
Diseases Ataxia Telangiectasia, Infection, Meningitis