M1CR0B1AL1Z3R 2.0: an enhanced web server for comparative analysis of bacterial genomes at scale
Yair Shimony, Edo Dotan, Elya Wygoda, Naama Wagner, Iris Lyubman, Noa Ecker, G. Durante, Gal Mishan, Jeff H. Chang, Oren Avram, Tal Pupko
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/.