ArticleNucleic acids research2025
M1CR0B1AL1Z3R 2.0: an enhanced web server for comparative analysis of bacterial genomes at scale.
Article in Nucleic acids research, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 5 papers.
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5 citing papers in PubMed.
- Identification of protein secretion systems and type III effectors in wood-associated bacteria of the genusMicrobiology spectrum · 2026Article
- Genome comparison of the bacteria in Mycobacterium avium complex (MAC) reveals the role of translational selection in shaping codon usage patterns.Molecular genetics and genomics : MGG · 2026Article
- Notes on the Description of Novel Prokaryotic Taxa.Current microbiology · 2026Article
- MCPmed: a call for Model Context Protocol-enabled bioinformatics web services for LLM-driven discovery.Briefings in bioinformatics · 2026Article
- Resolving taxonomic uncertainties in the genusFrontiers in microbiology · 2026Article
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Authors and funding
11 authors.
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Abstract
Large-scale analyses of bacterial genomic datasets contribute to the comprehensive characterization of complex microbial dynamics among different strains and species. Such analyses often include open reading frame extraction, orthogroup inference, phylogeny reconstruction, and functional annotation of proteins. We have previously developed the M1CR0B1AL1Z3R web server, a "one-stop shop" for conducting comparative analyses of microbial genomes. Here, we present M1CR0B1AL1Z3R 2.0, an enhanced version that includes a new user-friendly web interface and an improved, optimized, and more versatile pipeline. The following features were added: (i) a computationally efficient inference of orthogroups, which allows the analysis of up to 2000 bacterial genomes; (ii) genome completeness analysis; (iii) lists of orphan genes per genome; (iv) genome numeric representation that allows detecting genomic rearrangement events; (v) codon bias analysis; (vi) annotation of orthogroups with KEGG Orthology numbers; and (vii) a map of pairwise average nucleotide identity values. M1CR0B1AL1Z3R 2.0 is freely available at https://microbializer.tau.ac.il/.
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