ArticleBiology direct2012
Thousands of missed genes found in bacterial genomes and their analysis with COMBREX.
Article in Biology direct, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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Who cites it
17 citing papers in PubMed, 31 citations in OpenAlex.
- Proteins à la carte: riboproteogenomic exploration of bacterial N-terminal proteoform expression.mBio · 2024Article
- StORF-Reporter: finding genes between genes.Nucleic acids research · 2023Article
- Taxonomically Restricted Genes in Bacillus may Form Clusters of Homologs and Can be Traced to a Large Reservoir of Noncoding Sequences.Genome biology and evolution · 2023Article
- Lost and Found: Re-searching and Re-scoring Proteomics Data Aids Genome Annotation and Improves Proteome Coverage.mSystems · 2020Article
- System-level understanding of gene expression and regulation for engineering secondary metabolite production in Streptomyces.Journal of industrial microbiology & biotechnology · 2020Review
- Review
- OCCAM: prediction of small ORFs in bacterial genomes by means of a target-decoy database approach and machine learning techniques.Database : the journal of biological databases and curation · 2020Article
- Gene Unprediction with Spurio: A tool to identify spurious protein sequences.F1000Research · 2018Article
- Identification of Unannotated Small Genes inG3 (Bethesda, Md.) · 2017Article
- COMBREX-DB: an experiment centered database of protein function: knowledge, predictions and knowledge gaps.Nucleic acids research · 2016Article
- Evidence for the recent origin of a bacterial protein-coding, overlapping orphan gene by evolutionary overprinting.BMC evolutionary biology · 2015Article
- Quantitative frame analysis and the annotation of GC-rich (and other) prokaryotic genomes. An application to Anaeromyxobacter dehalogenans.Bioinformatics (Oxford, England) · 2015Article
- Determining microbial products and identifying molecular targets in the human microbiome.Cell metabolism · 2014Review
- SearchDOGS bacteria, software that provides automated identification of potentially missed genes in annotated bacterial genomes.Journal of bacteriology · 2014Article
- Activation and identification of five clusters for secondary metabolites in Streptomyces albus J1074.Microbial biotechnology · 2014Article
- eCAMBer: efficient support for large-scale comparative analysis of multiple bacterial strains.BMC bioinformatics · 2014Article
- Objective: biochemical function.Frontiers in genetics · 2014Article
Corrections and comments
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Authors and funding
10 authors at 4 institutions in 1 country.
Funding
Abstract
backgroundThe dramatic reduction in the cost of sequencing has allowed many researchers to join in the effort of sequencing and annotating prokaryotic genomes. Annotation methods vary considerably and may fail to identify some genes. Here we draw attention to a large number of likely genes missing from annotations using common tools such as Glimmer and BLAST.
resultsBy analyzing 1,474 prokaryotic genome annotations in GenBank, we identify 13,602 likely missed genes that are homologs to non-hypothetical proteins, and 11,792 likely missed genes that are homologs only to hypothetical proteins, yet have supporting evidence of their protein-coding nature from COMBREX, a newly created gene function database. We also estimate the likelihood that each potential missing gene found is a genuine protein-coding gene using COMBREX.
conclusionsOur analysis of the causes of missed genes suggests that larger annotation centers tend to produce annotations with fewer missed genes than smaller centers, and many of the missed genes are short genes <300 bp. Over 1,000 of the likely missed genes could be associated with phenotype information available in COMBREX. 359 of these genes, found in pathogenic organisms, may be potential targets for pharmaceutical research. The newly identified genes are available on COMBREX's website. REVIEWERS: This article was reviewed by Daniel Haft, Arcady Mushegian, and M. Pilar Francino (nominated by David Ardell).
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