Identification and characterization of epicuticular proteins of nematodes sharing motifs with cuticular proteins of arthropods
Cite this dataset
Betschart, Bruno; Bisoffi, Marco; Alaeddine, Ferial (2022). Identification and characterization of epicuticular proteins of nematodes sharing motifs with cuticular proteins of arthropods [Dataset]. Dryad. https://doi.org/10.5061/dryad.fttdz08vs
Abstract
Methods
The public accessible cDNA (X92101.2, 31B1A; AJ408885.1, C1; AJ408886.1, C2; AJ408887.1, C3) and genomic clones (AJ408888.1, G1; AJ408889.1, G2; AJ408890.1, G3), coding for A.suum epicuticlins, were used for a comparison of their common properties through alignments using Jalview. Based on the conserved common characteristics (aagaggaa), nucleotide Blasts were carried out on the following databases: NCBI (https://blast.ncbi.nlm.nih.gov/Blast.cgi) nucleotide collection, whole-genome shotgun contigs (wgs) of A. suum; WormbaseParasite and the EMBL-EBI services. Protein Blasts were carried out again on the same platforms and also using the protein knowledge platform UniProt. Multiple or pairwise nucleotide or protein sequence alignments were carried out using the EMBL-EBI services: Clustal Omega for multiple alignments and Needle or Matcher for pairwise alignments. Radar was used for the automatic alignment of protein repeats and Phobius to identify signal peptides. For the analysis of the C. elegans genes, Wormbase was the authoritative data source. Following Expasy services (https://www.expasy.org/) were applied for the in-depth study of the epicuticlins: STRING, ProtParam and Compute pI/MW.
Funding
Swiss National Science Foundation
University of Neuchâtel
Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung, Award: 008439
Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung, Award: 26764
Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung, Award: 33961
Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung, Award: 047194