Computational protocol: Detection of Anopheles rivulorum-like, a member of the Anopheles funestus group, in South Africa

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Protocol publication

[…] DNA was extracted from three specimens that were suspected to be An. rivulorum-like, using prepGEM® DNA Extraction Kits (ZyGEM™). The internal transcribed spacer region 2 (ITS2), which is the noncoding region between the 5.8S and 28S coding region of the specimens was amplified by PCR according to the protocol by Koekemoer et al. [].Subsequently, the PCR products of the ITS2 region from the three specimens were purified and sequenced by Macrogen Inc. The chromatograms of the sequences were analysed by using BioEdit version 7.2.5 []. The resulting sequences of the 3 specimens were compared to each other by using the Muscle multiple sequence alignment [] and a consensus sequence was established. Subsequently, the Emboss Needle pairwise sequence alignment tool [] was used to compare the consensus sequence with An. rivulorum-like sequences with the following GenBank accession numbers: KR014818 [], JN994147 [] and AF210725 [] as well as an An. rivulorum sequence GenBank accession number JN994148 []. […]

Pipeline specifications

Software tools BioEdit, MUSCLE, EMBOSS
Application Nucleotide sequence alignment
Organisms Anopheles gambiae, Anopheles funestus, Plasmodium falciparum
Diseases Malaria