A Comprehensive Bioinformatics Resource Guide for Genome-Based Antimicrobial Resistance Studies

Debyani Samantray, Ankit Singh Tanwar, Thokur Sreepathy Murali, Angela Brand, Kapaettu Satyamoorthy, Bobby Paul

Research output: Contribution to journalReview articlepeer-review


The use of high-throughput sequencing technologies and bioinformatic tools has greatly transformed microbial genome research. With the help of sophisticated computational tools, it has become easier to perform whole genome assembly, identify and compare different species based on their genomes, and predict the presence of genes responsible for proteins, antimicrobial resistance, and toxins. These bioinformatics resources are likely to continuously improve in quality, become more user-friendly to analyze the multiple genomic data, efficient in generating information and translating it into meaningful knowledge, and enhance our understanding of the genetic mechanism of AMR. In this manuscript, we provide an essential guide for selecting the popular resources for microbial research, such as genome assembly and annotation, antibiotic resistance gene profiling, identification of virulence factors, and drug interaction studies. In addition, we discuss the best practices in computer-oriented microbial genome research, emerging trends in microbial genomic data analysis, integration of multi-omics data, the appropriate use of machine-learning algorithms, and open-source bioinformatics resources for genome data analytics.

Original languageEnglish
Pages (from-to)445-460
Number of pages16
JournalOmics : a journal of integrative biology
Issue number10
Publication statusPublished - 01-10-2023

All Science Journal Classification (ASJC) codes

  • Biotechnology
  • Biochemistry
  • Molecular Medicine
  • Molecular Biology
  • Genetics


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