Computational protocol: HCV Infection among Saudi Population: High Prevalence of Genotype 4 and Increased Viral Clearance Rate

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Protocol publication

[…] BLAST analyses were initially performed to establish UTR5′ sequence identities to GenBank accessions. Comparative analyses were performed using the CLUSTAL W Multiple Sequence Alignment Program, Mega 4.1. HCV representative sequences used for the alignments were obtained from the GenBank and EMBL database. The phylogenetic trees were constructed by using the neighbour-joining method with Kimura two-parameter distances using MEGA version 4.1 . The reliability of internal branches was assessed by 1000 bootstrap replications and the p-distance substitution model. […]

Pipeline specifications

Software tools Clustal W, MEGA
Application Phylogenetics
Organisms Classical swine fever virus, Homo sapiens
Diseases Infection, Liver Diseases, HIV Infections