Nucleic acid or amino acid sequences, from import and assembly over multiple alignment to annotation, SNP analysis, primer design and comparison of complete chromosomes.
This tutorial explains how to use the BIONUMERICS emm typing script, developed for BIONUMERICS users that want to type Streptococcus pyogenes based on the portion of the emm gene that dictates the M serotype. The script assigns the emm type and subtype to imported (and assembled) sequences, by querying the CDC M-type specific database (ftp://ftp.cdc.gov/pub/infectious_diseases/biotech/tsemm/).
In this tutorial we will screen whole genome sequences of S. aureus samples for phenotypic traits such as virulence and antibiotic resistance using the S. aureus functional genotyping plugin. The plugin also allows you to detect phages and to extract MLST and spa repeat sequences.
This tutorial illustrates how to install and use the BIONUMERICS Sequence typing plugin for polymorphic VNTRs.
This tutorial illustrates how to calculate a multiple alignment and perform a mutation analysis in BIONUMERICS.
In this tutorial we will screen whole genome sequences of Salmonella samples for phenotypic traits using the Salmonella functional genotyping plugin. Phenotypic traits include: serotype, virulence and antibiotic resistance. The plugin also allows you to detect phages.
The BIONUMERICS SARS-CoV-2 plugin facilitates the processing and analysis of SARS-CoV-2 genomic sequences, whether downloaded from a public data repository or generated locally. In this plugin manual, all features of the SARS-CoV-2 plugin are covered, starting from the installation of the plugin, the import of genomic sequences, and all available analysis tools such as subsequence extraction and SNP analysis.
This tutorial demonstrates a RAxML(1) and FastTree(2) analysis on a multiple alignment in a BIONUMERICS database.
(1): Alexandros Stamatakis. Raxml version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics, 30(9):1312–1313, 2014. (2): Morgan N Price, Paramvir S Dehal, and Adam P Arkin. Fasttree 2–approximately maximumlikelihood trees for large alignments. PloS one, 5(3), 2010.
In this tutorial we will screen whole genome sequences of Mycobacterium tuberculosis complex samples for phenotypic traits using the Mycobacterium tuberculosis complex functional genotyping plugin. Phenotypic traits include: spoligotype, lineage and antibiotic resistance. The plugin also allows you to perform species confirmation.
In this tutorial we will screen whole genome sequences of Listeria samples for phenotypic traits using the Listeria functional genotyping plugin. Phenotypic traits include: serotype, virulence, and detergent and antibiotic resistance. The plugin also allows you to detect phages.
This tutorial shows the user how to create and validate an identification project based on a set of reference strains and how to use this reference set to identify unknown samples. Here, we use the 16s rDNA sequences, but any type of data and also combinations of data can be used in an identification project.