Genomics

Phylogenetic tree

Bacterial genome size

Bioinformatics

Scripting language

Biology

Gene

Comparative genomics

Operating system

Interface (matter)

The Internet

Web server

World Wide Web

Metagenomics

Genome

Programming language

Annotation

Graphical user interface

Computer science

Computational biology

Genetics

Gibbs isotherm

Biochemistry

Pulmonary surfactant

Application programming interface

Nucleic Acids Research

Large-scale mining and analysis of bacterial datasets contribute to the comprehensive characterization of complex microbial dynamics within a microbiome and among different bacterial strains, e.g., during disease outbreaks. The study of large-scale bacterial evolutionary dynamics poses many challenges. These include data-mining steps, such as gene annotation, ortholog detection, sequence alignment and phylogeny reconstruction. These steps require the use of multiple bioinformatics tools and ad-hoc programming scripts, making the entire process cumbersome, tedious and error-prone due to manual handling. This motivated us to develop the M1CR0B1AL1Z3R web server, a 'one-stop shop' for conducting microbial genomics data analyses via a simple graphical user interface. Some of the features implemented in M1CR0B1AL1Z3R are: (i) extracting putative open reading frames and comparative genomics analysis of gene content; (ii) extracting orthologous sets and analyzing their size distribution; (iii) analyzing gene presence-absence patterns; (iv) reconstructing a phylogenetic tree based on the extracted orthologous set; (v) inferring GC-content variation among lineages. M1CR0B1AL1Z3R facilitates the mining and analysis of dozens of bacterial genomes using advanced techniques, with the click of a button. M1CR0B1AL1Z3R is freely available at https://microbializer.tau.ac.il/.

M1CR0B1AL1Z3R—a user-friendly web server for the analysis of large-scale microbial genomics data