Early terminated transcripts and missing proteins reflect artifacts in bacterial proteomes
- 1European Molecular Biology Laboratory, European Bioinformatics Institute , Wellcome Genome Campus, Hinxton CB10 1SD ,
- 2Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine , Charlottesville, VA 22908 ,
Abstract
The high redundancy of many bacterial proteomes can be used to evaluate proteome quality and identify sequence errors. We have used MMseqs2 clustering with subsequent filtering to identify clusters that contain sequences from at least 50% of the clustered proteomes to build sets of core proteins that include proteins from 95% of the clustered bacteria. These clusters typically capture >80% of proteins in the bacteria. Because these clusters have highly uniform length (the median cluster has >99% of its proteins at the mode length), short (<75% of mode length) or long (>133%) proteins are likely artifacts. Most “outlier” proteins are found in fewer than 10% of clusters, and “high-outlier” clusters are over-represented in a small fraction of proteomes, which often have poor proteome BUSCO fragment scores. Short-outlier proteins are artifacts; at least 80% of short-outlier genomes contain mode-length copies of the protein, which were missed because of frameshifts, termination codons, or initiation codon choice. MMseqs2 clustering with 50% participation provides robust sets of core bacterial proteins and can be used to identify lower-quality proteomes and proteins.
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BibTeX
@article{insana2026early,
title = {{Early terminated transcripts and missing proteins reflect artifacts in bacterial proteomes}},
author = {Giuseppe Insana and Maria J Martin and William R Pearson},
journal = {NAR Genomics and Bioinformatics},
year = {2026},
month = nov,
doi = {10.1093/nargab/lqag129},
url = {https://academic.oup.com/nargab/article/doi/10.1093/nargab/lqag129/9013028},
note = {CC BY 4.0},
}
RIS
TY - JOUR
TI - Early terminated transcripts and missing proteins reflect artifacts in bacterial proteomes
AU - Giuseppe Insana
AU - Maria J Martin
AU - William R Pearson
PY - 2026
DA - 2026/11/05
JO - NAR Genomics and Bioinformatics
DO - 10.1093/nargab/lqag129
UR - https://academic.oup.com/nargab/article/doi/10.1093/nargab/lqag129/9013028
AB - The high redundancy of many bacterial proteomes can be used to evaluate proteome quality and identify sequence errors. We have used MMseqs2 clustering with subsequent filtering to identify clusters that contain sequences from at least 50% of the clustered proteomes to build sets of core proteins that include proteins from 95% of the clustered bacteria. These clusters typically capture >80% of proteins in the bacteria. Because these clusters have highly uniform length (the median cluster has >99% of its proteins at the mode length), short (<75% of mode length) or long (>133%) proteins are likely artifacts. Most “outlier” proteins are found in fewer than 10% of clusters, and “high-outlier” clusters are over-represented in a small fraction of proteomes, which often have poor proteome BUSCO fragment scores. Short-outlier proteins are artifacts; at least 80% of short-outlier genomes contain mode-length copies of the protein, which were missed because of frameshifts, termination codons, or initiation codon choice. MMseqs2 clustering with 50% participation provides robust sets of core bacterial proteins and can be used to identify lower-quality proteomes and proteins.
SN - 2631-9268
ER -