Computational protocol: Low major histocompatibility complex class II DQA diversity in the Giant Panda (Ailuropoda melanoleuca)

Similar protocols

Protocol publication

[…] All nucleotide and amino acid sequences were aligned using ClustalW. MEGA2.1 version was used to estimate the number of synonymous nucleotide substitutions per synonymous site (dS) and the number of nonsynonymous nucleotide substitutions per nonsynonymous site (dN) using the Nei and Gojobori method with a Jukes-Cantor correction []. These calculations were performed independently for the nucleotides within and outside the antigen-binding-sites (ABS) []). The ABS and non-ABS of these sequences were assigned after Paliakasis et al. [] in accordance with human HLA DQA molecule. Expected heterozygosity was calculated after Nei [] with the small sample size correction and deviation from the Hardy-Weinberg equilibrium was tested using Markov chain permutation test of 100 000 steps in GENEPOP version 3.4 []. ARLEQUIN version 2.0 [] was utilized to calculate Fst indices and the significance was tested using 1000 permutations. […]

Pipeline specifications

Software tools Clustal W, MEGA, Genepop, Arlequin
Application Population genetic analysis
Organisms Ailuropoda melanoleuca
Diseases Giant Cell Tumors