Computational protocol: Haemonchus contortus P-Glycoproteins Interact with Host Eosinophil Granules: A Novel Insight into the Role of ABC Transporters in Host-Parasite Interaction

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Protocol publication

[…] Database searches were performed using the Haemonchus contortus blast server (http://www.sanger.ac.uk/cgi-bin/blast/submitblast/h_contortus) and the BLAST Network Service (National Center for Biotechnology Information), using the BLASTX algorithm .The nucleotide sequences (Genbank-accession numbers are provided in ) were translated and amino acids sequences were aligned using MUSCLE . The corresponding nucleotide alignments were obtained by concatenating codons using the REVTRANS server (http://www.cbs.dtu.dk/services/RevTrans/) . The model of nucleotide substitution that best fitted the data was determined using jModeltest version 2.0 on the Phylemon 2 server .Phylogenetic relationships between Pgp sequences were defined for all the full length nucleotide sequences using the split-decomposition method implemented in SPLITSTREE version 4.11.3 using the general time reversible (GTR) scheme of substitution with a gamma distribution model of site rates variation (jModeltest results). […]

Pipeline specifications

Software tools BLASTX, MUSCLE, RevTrans, jModelTest, Phylemon, SplitsTree
Applications Phylogenetics, Nucleotide sequence alignment
Organisms Ovis aries, Haemonchus contortus, Homo sapiens, Caenorhabditis elegans
Diseases Infection