Computational protocol: Development of nested polymerase chain reaction-based diagnosis of duck enteritis virus and detection of DNA polymerase gene from non-descriptive duck breeds of West Bengal, India

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Protocol publication

[…] For the further experiment, nested PCR sample (Hoogly isolates) was sent to Xcelris Laboratory, Ahmedabad for sequencing in an automated DNA sequencer. The nucleotide sequence generated in this study has been deposited in EMBL (nested PCR product) database to obtain accession number. Data analysis and multiple alignments were performed using ClustalX [] and MEGA6 software []. The sequence was compared with GenBank database using the BLASTn. The evolutionary distances were computed using the p-distance method []. The confidence values of the internal rods were calculated by performing 1000 bootstrap analyses []. Phylogenetic tree for nucleotide sequences was drawn using the neighbor-joining method []. […]

Pipeline specifications

Software tools Clustal W, MEGA, BLASTN
Application Phylogenetics
Organisms Anas platyrhynchos
Chemicals Nucleotides