Automated reconstruction of reproducible protein databases with RepDBmaker.
4 affiliations
- 1Barcelona Supercomputing Centre (BSC-CNS), Barcelona, Spain.
- 2Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain.
- 3Catalan Institution for Research and Advanced Studies (ICREA), Barcelona, Spain.
- 4CIBER de Enfermedades Infecciosas, Instituto de Salud Carlos III, Madrid, Spain.
Abstract
RepDBmaker is a reproducible Snakemake pipeline designed for the automated construction of large-scale protein sequence databases. It enables the seamless downloading of sequences from different public databases and the integration of user-specified proteomes. The pipeline also performs standardized taxonomic annotations to all compiled sequences and contamination screening in eukaryotic proteomes. In addition, RepDBmaker generates queryable database files for Basic Local Alignment Search Tool Program (BLASTP), DIAMOND, and MMseqs2, with the option of taxonomy-aware sequence clustering to produce less redundant datasets. To showcase its utility, we used RepDBmaker to build a Tree-of-Life-scale database comprising 482 million protein sequences from 160,045 publicly available genomes and transcriptomes. RepDBmaker offers an off-the-shelf but customizable solution for researchers undertaking large-scale evolutionary projects that require extensive, well-annotated protein databases. The pipeline is available at https://github.com/Gabaldonlab/RepDBmaker.
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BibTeX
@article{mutti2026automated,
title = {{Automated reconstruction of reproducible protein databases with RepDBmaker.}},
author = {Giacomo Mutti and Toni Gabaldón},
journal = {Protein science : a publication of the Protein Society},
year = {2026},
month = oct,
doi = {10.1002/pro.70823},
url = {https://europepmc.org/article/MED/42905725},
note = {CC BY-NC},
}
RIS
TY - JOUR
TI - Automated reconstruction of reproducible protein databases with RepDBmaker.
AU - Giacomo Mutti
AU - Toni Gabaldón
PY - 2026
DA - 2026/10/30
JO - Protein science : a publication of the Protein Society
DO - 10.1002/pro.70823
UR - https://europepmc.org/article/MED/42905725
AB - RepDBmaker is a reproducible Snakemake pipeline designed for the automated construction of large-scale protein sequence databases. It enables the seamless downloading of sequences from different public databases and the integration of user-specified proteomes. The pipeline also performs standardized taxonomic annotations to all compiled sequences and contamination screening in eukaryotic proteomes. In addition, RepDBmaker generates queryable database files for Basic Local Alignment Search Tool Program (BLASTP), DIAMOND, and MMseqs2, with the option of taxonomy-aware sequence clustering to produce less redundant datasets. To showcase its utility, we used RepDBmaker to build a Tree-of-Life-scale database comprising 482 million protein sequences from 160,045 publicly available genomes and transcriptomes. RepDBmaker offers an off-the-shelf but customizable solution for researchers undertaking large-scale evolutionary projects that require extensive, well-annotated protein databases. The pipeline is available at https://github.com/Gabaldonlab/RepDBmaker.
SN - 0961-8368
SN - 1469-896X
ER -