Computational protocol: Genetic variations in regions of bovine and bovine-like enteroviral 5’UTR from cattle, Indian bison and goat feces

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Protocol publication

[…] For the short 5′UTR PCR fragments (286 bp) generated with the BEV detection primers, the nested PCR products of the expected size were excised from agarose gels, purified, and sequenced directly with the BEVseq-F primer. For the longer 5′UTR fragments (591 bp), the purified products were sequenced directly in both directions with the 41U18 and 611 L21 primers. The PCR products were purified with the GeneJET Gel Extraction Kit (Thermo Scientific) and the products were sequenced by a commercial DNA sequencing company (Macrogen, Seoul, Korea). The nucleotide sequence similarities were determined with the BLAST search algorithm, comparing the sample sequences with those in the National Center for Biotechnology Information (NCBI) GenBank nucleotide database. Sequence contigs derived from two-directional sequencing were joined with CAP (Contig Assembly Program) [] and the nucleotide sequences were aligned with ClustalW in BioEdit version 7.0.4.1. A phylogenetic tree was constructed in the MEGA 5 program, using the neighbor-joining algorithm with the Kimura two-parameter distance model and 1,000 bootstrap replicates []. Sequence identity was determined with the Sequence Identity Matrix function in BioEdit. […]

Pipeline specifications

Software tools Clustal W, BioEdit, MEGA
Application Phylogenetics
Organisms Capra hircus, Bos taurus, Enterovirus E, Viruses, Bos gaurus