ArticlePloS one2012
Predicting statistical properties of open reading frames in bacterial genomes.
Article in PloS one, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
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12 citing papers in PubMed, 34 citations in OpenAlex.
- Statistical analysis of synonymous and stop codons in pseudo-random and real sequences as a function of GC content.Scientific reports · 2023Article
- StringFix: an annotation-guided transcriptome assembler improves the recovery of amino acid sequences from RNA-Seq reads.Genes & genomics · 2023Article
- Three Novel Antisense Overlapping Genes in E. coli O157:H7 EDL933.Microbiology spectrum · 2023Article
- Article
- ORFik: a comprehensive R toolkit for the analysis of translation.BMC bioinformatics · 2021Article
- A Novel pH-Regulated, Unusual 603 bp Overlapping Protein Coding GeneFrontiers in microbiology · 2020Article
- Are Antisense Proteins in Prokaryotes Functional?Frontiers in molecular biosciences · 2020Article
- Unraveling the hidden universe of small proteins in bacterial genomes.Molecular systems biology · 2019Article
- Genomewide characterisation of the genetic diversity of carotenogenesis in bacteria of the order Sphingomonadales.Microbial genomics · 2018Article
- A novel short L-arginine responsive protein-coding gene (laoB) antiparallel overlapping to a CadC-like transcriptional regulator in Escherichia coli O157:H7 Sakai originated by overprinting.BMC evolutionary biology · 2018Article
- Evidence for the recent origin of a bacterial protein-coding, overlapping orphan gene by evolutionary overprinting.BMC evolutionary biology · 2015Article
- SearchDOGS bacteria, software that provides automated identification of potentially missed genes in annotated bacterial genomes.Journal of bacteriology · 2014Article
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Authors and funding
5 authors at 3 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
An analytical model based on the statistical properties of Open Reading Frames (ORFs) of eubacterial genomes such as codon composition and sequence length of all reading frames was developed. This new model predicts the average length, maximum length as well as the length distribution of the ORFs of 70 species with GC contents varying between 21% and 74%. Furthermore, the number of annotated genes is predicted with high accordance. However, the ORF length distribution in the five alternative reading frames shows interesting deviations from the predicted distribution. In particular, long ORFs appear more often than expected statistically. The unexpected depletion of stop codons in these alternative open reading frames cannot completely be explained by a biased codon usage in the +1 frame. While it is unknown if the stop codon depletion has a biological function, it could be due to a protein coding capacity of alternative ORFs exerting a selection pressure which prevents the fixation of stop codon mutations. The comparison of the analytical model with bacterial genomes, therefore, leads to a hypothesis suggesting novel gene candidates which can now be investigated in subsequent wet lab experiments.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.