ArticleBioinformatics and biology insights2013
Computational small RNA prediction in bacteria.
Article in Bioinformatics and biology insights, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 24 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
24 citing papers in PubMed, 40 citations in OpenAlex.
- Identification of Small RNAs inInternational journal of molecular sciences · 2024Article
- Devising Isolation Forest-Based Method to Investigate the sRNAome ofBioinformatics and biology insights · 2024Article
- High-Resolution Small RNAs Landscape Provides Insights into Alkane Adaptation in the Marine Alkane-Degrader Alcanivorax dieselolei B-5International journal of molecular sciences · 2022Article
- Non-Coding RNAs in Tuberculosis Epidemiology: Platforms and Approaches for Investigating the Genome's Dark Matter.International journal of molecular sciences · 2022Review
- TheFrontiers in molecular biosciences · 2022Review
- Ms1 RNA Interacts With the RNA Polymerase Core inFrontiers in microbiology · 2022Article
- PresRAT: a server for identification of bacterial small-RNA sequences and their targets with probable binding region.RNA biology · 2021Article
- Pan-Genome of the GenusFrontiers in microbiology · 2021Article
- Prevalence of small base-pairing RNAs derived from diverse genomic loci.Biochimica et biophysica acta. Gene regulatory mechanisms · 2020Review
- Altered Fecal Small RNA Profiles in Colorectal Cancer Reflect Gut Microbiome Composition in Stool Samples.mSystems · 2019Article
- Functional annotation and distribution overview of RNA families in 27 Streptococcus agalactiae genomes.BMC genomics · 2018Article
- Small RNA repertoires and their intraspecies variation in Aggregatibacter actinomycetemcomitans.DNA research : an international journal for rapid publication of reports on genes and genomes · 2018Article
- Article
- Comparative genomics of microsporidian genomes reveals a minimal non-coding RNA set and new insights for transcription in minimal eukaryotic genomes.DNA research : an international journal for rapid publication of reports on genes and genomes · 2017Article
- An improved method for identification of small non-coding RNAs in bacteria using support vector machine.Scientific reports · 2017Article
- A Genome-Wide Prediction and Identification of Intergenic Small RNAs by Comparative Analysis inFrontiers in microbiology · 2017Article
- Analysis of Small RNAs in Streptococcus mutans under Acid Stress-A New Insight for Caries Research.International journal of molecular sciences · 2016Article
- A computational strategy for the search of regulatory small RNAs in Actinobacillus pleuropneumoniae.RNA (New York, N.Y.) · 2016Article
- Transcriptomic analysis of staphylococcal sRNAs: insights into species-specific adaption and the evolution of pathogenesis.Microbial genomics · 2016Article
- Towards the complete small RNome ofMicrobial genomics · 2016Article
Corrections and comments
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Authors and funding
2 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Bacterial, small RNAs were once regarded as potent regulators of gene expression and are now being considered as essential for their diversified roles. Many small RNAs are now reported to have a wide array of regulatory functions, ranging from environmental sensing to pathogenesis. Traditionally, noncoding transcripts were rarely detected by means of genetic screens. However, the availability of approximately 2200 prokaryotic genome sequences in public databases facilitates the efficient computational search of those molecules, followed by experimental validation. In principle, the following four major computational methods were applied for the prediction of sRNA locations from bacterial genome sequences: (1) comparative genomics, (2) secondary structure and thermodynamic stability, (3) 'Orphan' transcriptional signals and (4) ab initio methods regardless of sequence or structure similarity; most of these tools were applied to locate the putative genomic sRNA locations followed by experimental validation of those transcripts. Therefore, computational screening has simplified the sRNA identification process in bacteria. In this review, a plethora of small RNA prediction methods and tools that have been reported in the past decade are discussed comprehensively and assessed based on their attributes, compatibility, and their prediction accuracy.
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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.