Computational protocol: Broad Spectrum Antimicrobial Activity of Forest-Derived Soil Actinomycete, Nocardia sp. PB-52

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Protocol publication

[…] Identification of phylogenetic neighbors and calculation of pairwise sequence similarities of 16S rRNA gene of PB-52 strain were carried out using BLASTN (Altschul et al., ) and EzTaxon server (http://www.eztaxon.org/; Kim et al., ). Top 14 reference sequences with highest scores were selected for multiple sequence alignment which was performed by CLUSTAL W program (Thompson et al., ). The phylogenetic tree was constructed by neighbor-joining method (Saitou and Nei, ) using MEGA version 4.0 (Tamura et al., ). The support of each clade was determined by bootstrap analysis performed with 1000 replications (Felsenstein, ). The GenBank accession number for the partial 16S rRNA gene sequence of PB-52 strain is KM406386. […]

Pipeline specifications

Software tools BLASTN, Clustal W, MEGA
Databases EzBioCloud
Application Phylogenetics
Organisms Saccharomyces cerevisiae, Epipremnum aureum, Klebsiella pneumoniae, Bacteria, Staphylococcus aureus
Diseases Nocardia Infections, Staphylococcal Infections