Computational protocol: Genomic organization and recombination analysis of a porcine sapovirus identified from a piglet with diarrhea in China

Similar protocols

Protocol publication

[…] Similarity searches of the sequences were carried out in BLAST (http://www.ncbi.nlm.nih.gov/BLAST/). After a multiple alignment with CLUSTAL W embedded in MEGA 7, the phylogenetic relationship of the strain in the present study and the reference sequences were assessed using MEGA 7. For analysis in MEGA 7, Jukes-cantor (JC) distance was utilized, employing the Neighbor joining (NJ) algorithm []. The reliability of different phylogenetic groupings was evaluated by using the bootstrap test (1000 bootstrap replications) available in MEGA 7. The identification of recombinants was performed by using the Recombination Detection Program 4 (RDP 4) (http://darwin.uvigo.es/rdp/rdp.html) []. Prototype SaV strains used as references in the analysis with their corresponding GenBank accession numbers, source of origin and genogroups are showed in Table . […]

Pipeline specifications

Software tools Clustal W, MEGA, RDP4
Application Phylogenetics
Organisms Sus scrofa, Homo sapiens, Porcine circovirus 2, Transmissible gastroenteritis virus
Diseases Gastroenteritis, HIV Infections
Chemicals Nucleotides