Computational protocol: The Echinococcus granulosus Antigen B Gene Family Comprises at Least 10 Unique Genes in Five Subclasses Which Are Differentially Expressed

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Protocol publication

[…] Inspection of the amino-acid sequences inferred from data collected during this study and obtained from the public databases showed that some members of the EgAgB subfamily could be aligned with ease. However, sequences from other subfamilies of EgAgB and sequences from other cestodes proved more difficult to align. Furthermore any alignment would be short: 54 amino acids being the length of the shortest sequence. However, to produce a graphical representation of the data, we constructed a simple phylogenetic tree to show the different clusters clearly, including relationships among members of each subfamily. We accept that such a tree does not provide robust inference for the deeper nodes. Bioedit (http://www.mbio.ncsu.edu/BioEdit/bioedit.html) was used to align sequences. Molecular Evolutionary Genetics Analysis version 4 (MEGA v4) program (http://www.megasoftware.net/) was used to construct the tree from amino acid sequences translated from the second exonic sequences of EgAgB amplified and cloned from E. granulosus in this study and homologous protein sequences from other cestode parasites deposited in the GenBank, EMBL and DDBJ databases, after removal of the signal peptides at their N terminal. A distance matrix was constructed using a Poisson correction method before a mid-point rooted tree was constructed by the minimum-evolution method. One thousand bootstrap cycles were used. […]

Pipeline specifications

Software tools BioEdit, MEGA, MEGA-V
Databases DDBJ
Applications Phylogenetics, GWAS
Organisms Echinococcus granulosus, Canis lupus familiaris