GTDB-Tk: a toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes.
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Updated
Sep 11, 2024 - Python
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
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.
Design clade-specific primers targeting a pan-genome core gene
A spin on the Tele* scripts, this time processing and comparing protein sequence input against those of Halobacterium genus
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.
*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
A library to get information on organisms and UniProt identifiers. This includes growth temperature, growth ph, pfam domains, taxonomic lineage.
Methanoperedens nitroreducens genome-scale metabolic model.
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