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Pathogenomics Analysis

Pathogenomics is a novel discipline that uses high-throughput screening technology and bioinformatics approaches to study encoded resistance and virulence factors (VFs), which enable a microorganism to infect a host and possibly cause disease. We present comparative analytical methods using a series of bioinformatics tools to provide information that can be used to combat pathogenic infections. 

Workflow Design Based on a Comparative Research Approach

Stage 1

  • Sequence reads processing and genome assembly  

  • Retrieval of the genome sequence of other strains for comparative analysis 

  • General genome features (tabular)

  • Comprehensive genome analysis (annotation/gene prediction; hypothetical and functional proteins, enzyme commission, genome features, protein features)

  • Subsystem functional categorization of query sample(s)

  • Genome sequence properties (tabular) of query sample and other comparative strains

Stage 2

  • Plasmid prediction of all assembly genomes

  • Prediction of a bacteria's pathogenicity towards human hosts.

  • ToxFinder: identification of genes involved in mycotoxin synthesis (optional)

  • Antimicrobial Resistance Profiling

  • Comparative AMR genes (prevalence of antibiotic-resistant genes per samples and classes of antibiotics, resistance gene distribution, frequency comparison, etc.)

  • Comparative resistant mechanism

  • Shared resistance genes between strains

  • The pattern of antimicrobial resistance in a region

Stage 3

  • Virulence Factors

  • Comparative virulence factors and genes between strains

  • Shared specific genes

  • Drug targets and Protein Structures (optional)

  • Mobile Gene Elements/Transporters

  • Genome Analysis

  • Pan-genome and core-genome analysis (genome map, orthologous genes, homologous genes)

  • Single Nucleotide Polymorphisms (SNPs)

  • Evolutionary study (Phylogenetic tree, ANI analysis)

Stage 4

  • Computing data and visualization of the results: (Statistical visualization which includes heatmaps, tabular, Venn diagram, bar charts, clusters, etc.)

  • Report (Materials and Method, Results and References)   

The workflow as we have shown you entails the steps of bioinformatics analysis to be carried out for your data and each is unique to the workflow designed for the final outcome. 

The analysis will be conducted providing your desired visualization for each major steps.

The following will be provided after the complete job is done.

  • Assembly genome sequence

  • A detailed draft of a report containing the materials and methods, results, and references

  • Visualizations (figures)

  • Technical support: A live zoom session will be held to explain and discuss the results with you. 

Get In Touch

You can book a free session with us to discuss what you want to do, your research project, and show you a demo report. We promise to deliver accurate and trusted work done.

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