ArticleJournal of mathematical biology2008
Prediction of small, noncoding RNAs in bacteria using heterogeneous data.
Article in Journal of mathematical biology, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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Who cites it
16 citing papers in PubMed.
- Devising Isolation Forest-Based Method to Investigate the sRNAome ofBioinformatics and biology insights · 2024Article
- PresRAT: a server for identification of bacterial small-RNA sequences and their targets with probable binding region.RNA biology · 2021Article
- Sequence-based bacterial small RNAs prediction using ensemble learning strategies.BMC bioinformatics · 2018Article
- Improving E. coli growth performance by manipulating small RNA expression.Microbial cell factories · 2017Review
- Article
- TargetRNA2: identifying targets of small regulatory RNAs in bacteria.Nucleic acids research · 2014Article
- Inferring the relation between transcriptional and posttranscriptional regulation from expression compendia.BMC microbiology · 2014Article
- Small regulatory RNAs in Archaea.RNA biology · 2014Review
- Using RNA inverse folding to identify IRES-like structural subdomains.RNA biology · 2013Article
- Directional RNA-seq reveals highly complex condition-dependent transcriptomes in E. coli K12 through accurate full-length transcripts assembling.BMC genomics · 2013Article
- Computational small RNA prediction in bacteria.Bioinformatics and biology insights · 2013Article
- nocoRNAc: characterization of non-coding RNAs in prokaryotes.BMC bioinformatics · 2011Article
- Non-coding RNA detection methods combined to improve usability, reproducibility and precision.BMC bioinformatics · 2010Article
- A genome-wide analysis of small regulatory RNAs in the human pathogen group A Streptococcus.PloS one · 2009Article
- Small non-coding RNAs in Streptomyces coelicolor.Nucleic acids research · 2008Article
- Deep sequencing-based identification of small non-coding RNAs in Streptomyces coelicolor.RNA biologyArticle
Corrections and comments
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Authors and funding
1 author.
Funding
Abstract
sRNAFinder is a new gene prediction system for systematic identification of noncoding genes in bacteria. Most noncoding RNAs in prokaryotes belong to a class of genes denoted as small RNAs (sRNAs). In the model organism Escherichia coli, over 70 sRNA genes have been identified, and the existence of many more has been hypothesized. While various sources of information have proven useful for prediction of novel sRNA genes, most computational approaches do not take advantage of the disparate sources of data available for identifying these noncoding RNA genes. We present a general probabilistic method for predicting sRNA genes in bacteria. The method, based on a general Markov model, is implemented in the computational tool sRNAFinder. sRNAFinder incorporates heterogeneous data sources for gene prediction, including primary sequence data, transcript expression data from microarray experiments, and conserved RNA structure information as determined from comparative genomics analysis. We demonstrate that sRNAFinder improves upon current tools for identifying small, noncoding genes in bacteria.
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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.