ArticleGenome research2017
An integrative strategy to identify the entire protein coding potential of prokaryotic genomes by proteogenomics.
Article in Genome research, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 44 papers.
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Who cites it
44 citing papers in PubMed, 86 citations in OpenAlex.
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- Detection and Quantitation of Small Proteins Using Mass Spectrometry.Molecular & cellular proteomics : MCP · 2025Article
- De novo gene birth and the conundrum of ORFan genes in bacteria.Genome research · 2025Review
- VirNucPro: an identifier for the identification of viral short sequences using six-frame translation and large language models.Briefings in bioinformatics · 2025Article
- How Small Proteins Adjust the Metabolism of Cyanobacteria Under Stress: The Role of Small Proteins in Cyanobacterial Stress Responses.BioEssays : news and reviews in molecular, cellular and developmental biology · 2025Review
- Uncovering the small proteome of Methanosarcina mazei using Ribo-seq and peptidomics under different nitrogen conditions.Nature communications · 2024Article
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- StORF-Reporter: finding genes between genes.Nucleic acids research · 2023Article
- Small proteins in Gram-positive bacteria.FEMS microbiology reviews · 2023Article
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- Detection of Known and Novel Small Proteins inAnalytical chemistry · 2023Article
- Unraveling the small proteome of the plant symbiontmicroLife · 2023Article
- Revealing the small proteome ofmicroLife · 2023Article
- An analysis of proteogenomics and how and when transcriptome-informed reduction of protein databases can enhance eukaryotic proteomics.Genome biology · 2022Article
- A Practical Guide to Small Protein Discovery and Characterization Using Mass Spectrometry.Journal of bacteriology · 2022Article
- Functional characterization of prokaryotic dark matter: the road so far and what lies ahead.Current research in microbial sciences · 2022Review
- Hidden in plain sight: challenges in proteomics detection of small ORF-encoded polypeptides.microLife · 2022Article
- Prokaryotic Genome Annotation.Methods in molecular biology (Clifton, N.J.) · 2022Article
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Authors and funding
14 authors at 4 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Accurate annotation of all protein-coding sequences (CDSs) is an essential prerequisite to fully exploit the rapidly growing repertoire of completely sequenced prokaryotic genomes. However, large discrepancies among the number of CDSs annotated by different resources, missed functional short open reading frames (sORFs), and overprediction of spurious ORFs represent serious limitations. Our strategy toward accurate and complete genome annotation consolidates CDSs from multiple reference annotation resources, ab initio gene prediction algorithms and in silico ORFs (a modified six-frame translation considering alternative start codons) in an integrated proteogenomics database (iPtgxDB) that covers the entire protein-coding potential of a prokaryotic genome. By extending the PeptideClassifier concept of unambiguous peptides for prokaryotes, close to 95% of the identifiable peptides imply one distinct protein, largely simplifying downstream analysis. Searching a comprehensive
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