Computational protocol: Identification of the Receptor and Cellular Ortholog of the Marek's Disease Virus (MDV) CXC Chemokine

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Protocol publication

[…] Amino acid sequences of MDV vIL-8 and all known chicken CXC chemokines were aligned using the ClustalW (Vector NTI 9.1, Invitrogen) and MEGA 6 software (Tamura et al., ). Phylogenetic analyses of vIL-8, chicken and human CXC chemokines were performed based on their amino acid sequences applying neighbor-joining (NJ), maximum-parsimony (MP), and maximum-likelihood (ML) methods using the MEGA 6 software (Tamura et al., ). Full length amino acid sequences of MDV vIL-8 (AAN60433.1), the known chicken CXC chemokines, cCXCL1 (XP_420608.1), cCXCL8L1 (NP_990349.1), cCXCL8L2 (NP_990829.1), cCXCL12 (NP_989841.1), CXCL13L1 (XP_004941081.1), CXCL13L2 (CCC15119.1), CXCL13L3 (CCC15120.1), cCXCL14 (NP_990043.1) and human CXC chemokine orthologues, hCXCL1 (AAH11976.1), hCXCL8 (NP_000575.1), hCXCL12 (AAH39893.1), hCXCL13 (AAH12589.1), hCXCL14 (XP_527018.2) were obtained from Genbank. […]

Pipeline specifications

Software tools Clustal W, Vector NTI Advance, MEGA
Applications Phylogenetics, Protein sequence analysis
Organisms Gallus gallus, Human poliovirus 1 Mahoney
Diseases Lymphoma, Marek Disease, HIV Infections
Chemicals Amino Acids