ArticleNucleic acids research2002
Searching for RNA genes using base-composition statistics.
Article in Nucleic acids research, 2002. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 52 papers.
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Who cites it
52 citing papers in PubMed, 109 citations in OpenAlex.
- Small Regulatory RNAs in Prokaryotes: Key Features, Identification, Environmental Roles, and Applications.Microorganisms · 2026Review
- The discovery of novel noncoding RNAs in 50 bacterial genomes.Nucleic acids research · 2024Article
- Comprehensive discovery of novel structured noncoding RNAs in 26 bacterial genomes.RNA biology · 2021Article
- Revisiting the Relationships Between Genomic G + C Content, RNA Secondary Structures, and Optimal Growth Temperature.Journal of molecular evolution · 2021Article
- A second riboswitch class for the enzyme cofactor NADRNA (New York, N.Y.) · 2021Article
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- A bacterial riboswitch class for the thiamin precursor HMP-PP employs a terminator-embedded aptamer.eLife · 2019Article
- Genome-wide discovery of structured noncoding RNAs in bacteria.BMC microbiology · 2019Article
- A comparative study of sequence- and structure-based features of small RNAs and other RNAs of bacteria.RNA biology · 2018Article
- Review
- Article
- Mechanistic Insights into Archaeal and Human Argonaute Substrate Binding and Cleavage Properties.PloS one · 2016Article
- Primary transcriptome map of the hyperthermophilic archaeon Thermococcus kodakarensis.BMC genomics · 2014Article
- Identification of non-coding RNAs with a new composite feature in the Hybrid Random Forest Ensemble algorithm.Nucleic acids research · 2014Article
- Generation and phenotyping of a collection of sRNA gene deletion mutants of the haloarchaeon Haloferax volcanii.PloS one · 2014Article
- Small regulatory RNAs in Archaea.RNA biology · 2014Review
- RNA at 92 °C: the non-coding transcriptome of the hyperthermophilic archaeon Pyrococcus abyssi.RNA biology · 2013Article
- Small RNAs for defence and regulation in archaea.Extremophiles : life under extreme conditions · 2012Review
- High throughput sequencing reveals a plethora of small RNAs including tRNA derived fragments in Haloferax volcanii.RNA biology · 2012Article
- An in silico model for identification of small RNAs in whole bacterial genomes: characterization of antisense RNAs in pathogenic Escherichia coli and Streptococcus agalactiae strains.Nucleic acids research · 2012Article
Corrections and comments
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Authors and funding
1 author at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The hypothesis that genomic regions rich in non-protein-coding RNAs (ncRNAs) can be identified using local variations in single-base and dinucleotide statistics has been investigated. (G+C)%, (G-C)% difference, (A-T)% difference and dinucleotide-frequency statistics were compared among seven classes of ncRNAs and three genomes. Significant variations were observed in (G+C)% and, in Methanococcus jannaschii, in the frequency of the dinucleotide 'CG'. Screening programs based on these two base-composition statistics were developed. With (G+C)% screening alone, a 1% fraction of the M.jannaschii genome containing all 44 known transfer RNAs, ribosomal RNAs and signal recognition particle RNAs could be identified. When (G+C)% combined with CG dinucleotide-frequency screening was used, 43 of the 44 known M.jannaschii structural ncRNAs were again identified, while the number of presumably false hits overlapping a known or putative protein-coding gene was reduced from 15 to 6. In addition, 19 candidate ncRNAs were identified including one with significant homology to several known archaeal RNaseP RNAs.
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Registered trials
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.