Computational protocol: Characterization of leptospira borgpetersenii isolates from field rats (rattus norvegicus) by 16s rrna and lipl32 gene sequencing

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Protocol publication

[…] The 16S rRNA and lipL32 gene sequences of the rat isolates and the highly identical sequences for 16S rRNA and lipL32, used in this study were retrieved from NCBI database using Basic Local Alignment Search Tool (BLASTn) and PSI-BLAST tool with default parameters. Sequences with more significant identity were aligned with ClustalW algorithm implemented in Molecular Evolutionary Genetics Analysis (MEGA 4.0) using Smith-Waterman substitution matrix and trimmed to consensus, and Unweighted Pair Group Method with Arithmetic Mean (UPMGA) trees were constructed with 1000 bootstraps at uniform divergence rates with Jukes and Cantor evolutionary model and 0.25 gamma distribution factors (). Gaps in the aligned sequences were replaced by Ns in BioEdit (). Posterior probability and conserved regions among closely related sequences were carried by MEGA 4.0 and BioEdit […]

Pipeline specifications

Software tools BLASTN, BLASTP, Clustal W, MEGA, BioEdit
Application Phylogenetics
Organisms Leptospira borgpetersenii, Rattus norvegicus
Diseases Leptospirosis