Computational protocol: A Pan-Lyssavirus Taqman Real-Time RT-PCR Assay for the Detection of Highly Variable Rabies virus and Other Lyssaviruses

Similar protocols

Protocol publication

[…] BioEdit software (http://www.mbio.ncsu.edu/BioEdit/bioedit.html) was used for the alignment of LN34 target sequences. N gene sequencing was performed as described by Hughes et al. 2006 []. Eighty-eight whole N gene nucleotide sequences included in the validation panel were subjected to multiple sequence alignments using CLUSTALW (http://www.ebi.ac.uk/clustalw/index.html). All sequences were edited to 1350 bp fragments using BioEdit () []. A similarity matrix was calculated using the 88 aligned sequences with MEGA 6 and is summarized in []. A phylogenetic tree was constructed using the full N gene sequences of the 88 samples in the validation panel and 104 sequences retrieved from GenBank () using the neighbor-joining method and Kimura-2 parameter substitution model with 1000 bootstrap replicates. […]

Pipeline specifications

Software tools BioEdit, Clustal W, MEGA
Application Phylogenetics
Organisms Rabies lyssavirus, Homo sapiens
Diseases Zoonoses, HIV Infections