Brownotate, a Comprehensive Solution to Generate Protein Sequence Databases for Any Species
Abstract
Proteomics is strengthening research in biology and the diversification of the model organisms studied is very promising for fully understanding the complexity of biological principles. However, the lack of protein sequence databases for many species is a major bottleneck. Existing computational solutions are usually incomplete and/or only usable by bioinformaticians. We have built an open-source, user-friendly pipeline, called Brownotate, which allows anyone to generate protein sequence databases for any species as long as sequencing information is available. The pipeline can extract already existing protein sequences, but also automatically annotate any genome assembly or assemble and annotate any DNA sequence dataset. By testing the pipeline with numerous sequencing and assembly datasets covering a large part of the phylogenetic tree, we show that Brownotate generates fragmented but good quality assemblies and good quality annotations when compared to reference data. By comparing the use of protein databases generated by Brownotate or downloaded from NCBI to interpret proteomic data, we show very comparable results. The Brownotate pipeline is, therefore, an important new addition to the proteomics toolbox.
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BibTeX
@article{brown2026brownotate,
title = {{Brownotate, a Comprehensive Solution to Generate Protein Sequence Databases for Any Species}},
author = {Adrien Brown and Alexandre Burel and Sarah Cianférani and Christine Carapito and Fabrice Bertile},
journal = {Proteomics},
year = {2026},
month = sep,
doi = {10.1002/pmic.70094},
url = {https://hal.science/hal-05771454v1},
note = {CC BY 4.0},
}
RIS
TY - JOUR
TI - Brownotate, a Comprehensive Solution to Generate Protein Sequence Databases for Any Species
AU - Adrien Brown
AU - Alexandre Burel
AU - Sarah Cianférani
AU - Christine Carapito
AU - Fabrice Bertile
PY - 2026
DA - 2026/09/30
JO - Proteomics
DO - 10.1002/pmic.70094
UR - https://hal.science/hal-05771454v1
AB - Proteomics is strengthening research in biology and the diversification of the model organisms studied is very promising for fully understanding the complexity of biological principles. However, the lack of protein sequence databases for many species is a major bottleneck. Existing computational solutions are usually incomplete and/or only usable by bioinformaticians. We have built an open-source, user-friendly pipeline, called Brownotate, which allows anyone to generate protein sequence databases for any species as long as sequencing information is available. The pipeline can extract already existing protein sequences, but also automatically annotate any genome assembly or assemble and annotate any DNA sequence dataset. By testing the pipeline with numerous sequencing and assembly datasets covering a large part of the phylogenetic tree, we show that Brownotate generates fragmented but good quality assemblies and good quality annotations when compared to reference data. By comparing the use of protein databases generated by Brownotate or downloaded from NCBI to interpret proteomic data, we show very comparable results. The Brownotate pipeline is, therefore, an important new addition to the proteomics toolbox.
SN - 1615-9853
SN - 1615-9861
ER -