Computational protocol: A novel blood-feeding detoxification pathway in Nippostrongylus brasiliensis L3 reveals a potential checkpoint for arresting hookworm development

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Protocol publication

[…] BlastP (v2.2.28, https://www.ncbi.nlm.nih.gov/pubmed/18440982) was used to identify Nb protein sequences obtained from the L3 & “L5” adult secretomes [] presenting high similarity to groups of selected target proteins of interest. BlastX (v2.2.28, https://www.ncbi.nlm.nih.gov/pubmed/18440982) was used to do the same for proteins translated from transcripts assembled from the iL3 transcriptome []. Top-scoring hits with alignments covering at least 95% of the Nb proteins were considered for further analysis. Two groups of target proteins of interest were defined: one including homologs of the Na-APR1 protein (see list below), and one including homologs of Na-GST1 protein (see list below). With these targets, 1 and 11 putative Nb protein homologs were manually identified from the Blast results, respectively. Proteins from each group were then aligned using Clustal Omega (v1.2.3, http://msb.embopress.org/content/7/1/539) with default settings for protein alignment. Multiple sequence alignments were visualised using the JalView 2 Desktop application (http://bioinformatics.oxfordjournals.org/content/25/9/1189). For the GST1 group, amino acids were visually coloured based on the ClustalX scheme. Molecular phylogenies were generated using Clustal Omega’s Phylogeny program using UPGMA clustering with distance correction (http://bioinformatics.oxfordjournals.org/content/23/21/2947.full), and were used to order sequences in the alignments. Finally, sequence features of interest were manually highlighted in the alignments. […]

Pipeline specifications

Software tools BLASTP, BLASTX, Clustal Omega, Jalview, Clustal W
Application Phylogenetics
Organisms Homo sapiens, Necator americanus, Canis lupus familiaris, Mus musculus, Caenorhabditis elegans, Rattus norvegicus
Diseases Anemia, Hookworm Infections