Computational protocol: Genetic Characterization of Feline Leukemia Virus from Florida Panthers

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Protocol publication

[…] Sequences from env and LTR were analyzed separately. For analysis relative to known domestic cat FeLV sequences, we included FeLV-945, FeLVA-3281, FeLVA-61E, FeLVA-Glasgow-1, FeLVC-Sarma, FeLVB-Rickard, SM-FeSV, enFeLV-AGTT (accession nos. AY662447, M18248, M18247, M12500, M14331, X00188, M23025, AY364318 respectively) (env) and FCA-945, FCA-934, FeLVA-3281, and FeLVA-Glasgow-1 (accession nos. AY374189, AY374184, M18248, and M12500, respectively) (LTR). Nucleotide sequences were compiled and aligned for subsequent phylogenetic analysis by ClustalX () and verified visually (). MODELTEST () was used for env and LTR analysis to estimate the optimal model of sequence evolution; these settings were incorporated into subsequent analyses. Minimum-evolution trees were constructed from models of substitution specified by MODELTEST; starting trees were obtained by the neighbor-joining method, followed by application of a tree-bisection-reconnection branch-swapping algorithm during a heuristic search for the optimal tree. Maximum-parsimony analysis used a heuristic search of starting trees obtained by stepwise addition and followed by tree-bisection-reconnection. Maximum likelihood parameters specified by MODELTEST selected the general time-reversible model of substitution; they included empirical base frequencies and estimated rate matrix and corrected for among-site rate variation (γ distribution). A bootstrap analysis that used 1,000 iterations was performed with each method. Amino acid residue alignments were generated by using MacClade 3.05 () and ClustalX. Sequences were inspected for homoplasies. Nucleotide sequences were translated to protein, and genetic distances were calculated in MEGA 3.0 () by using the Tajima-Nei (nucleotide) and Dayhoff (amino acid) algorithms. The sequences of FeLV-Pco env and LTR were deposited in GenBank under accession nos. EU189489–EU189498. […]

Pipeline specifications

Software tools Clustal W, ModelTest-NG, MacClade, MEGA
Application Phylogenetics
Organisms Puma concolor, Felis catus
Diseases Anemia, Lymphatic Diseases, HIV Infections, Leukemia, Feline