GTDB-Tk: a toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes.

A machine learning model for the prediction of optimal growth temperature of microorganisms and enzyme catalytic optima

🦠📇 Microbial genomes-to-report pipeline

This is a microbial amplicon sequence (16S and 18S iTag) data and analyses pipeline corresponding to the manuscript, "Community ecology across bacteria, archaea and microbial eukaryotes in the sediment and seawater of coastal Puerto Nuevo, Baja California" for public benefit and usage.

A library to get information on organisms and UniProt identifiers. This includes growth temperature, growth ph, pfam domains, taxonomic lineage.

Code and Data related to Wimmer and Morais et al (2023)

Design clade-specific primers targeting a pan-genome core gene

V. M. Gumerov, E. P. Andrianova, M. A. Matilla, Karen M. Page, Elizabet Monteagudo-Cascales, A. C. Dolphin, T. Krell, I. B. Zhulin (2022). Amino acid sensor conserved from bacteria to humans.

Curated mirror of RefSeq Microbial Genomes. Available via CVMFS repository.

Methanoperedens nitroreducens genome-scale metabolic model.

Final Project WS2019: Alexander Amberger, Matthias Gruber, Simone Zimmerl

Code that was used to generate figures for the Mahmoudi et al., 2013 publication

A spin on the Tele* scripts, this time processing and comparing protein sequence input against those of Halobacterium genus

Code from paper "Systematic genome-guided discovery of antagonistic interactions between archaea and bacteria"

*Cerna-Vargas J-P., *Gumerov V.M., Krell T., Zhulin I.B. (2023) Amine recognizing domain in diverse receptors from bacteria and archaea evolved from the universal amino acid sensor. PNAS, 120, e2305837120