ArticleBMC bioinformatics2011
nocoRNAc: characterization of non-coding RNAs in prokaryotes.
Article in BMC bioinformatics, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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18 citing papers in PubMed, 42 citations in OpenAlex.
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- In silico prediction and expression profile analysis of small non-coding RNAs in Herbaspirillum seropedicae SmR1.BMC genomics · 2020Article
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- Applying a New REFINE Approach inFrontiers in microbiology · 2019Article
- Functional annotation and distribution overview of RNA families in 27 Streptococcus agalactiae genomes.BMC genomics · 2018Article
- Article
- Non-Coding RNAs are Differentially Expressed byThe open microbiology journal · 2017Article
- Whole Genome Shotgun Sequencing Shows Selection on Leptospira Regulatory Proteins During in vitro Culture Attenuation.The American journal of tropical medicine and hygiene · 2016Article
- The Pathway-Specific Regulator ClaR of Streptomyces clavuligerus Has a Global Effect on the Expression of Genes for Secondary Metabolism and Differentiation.Applied and environmental microbiology · 2015Article
- Characterization of a mazEF toxin-antitoxin homologue from Staphylococcus equorum.Journal of bacteriology · 2013Article
- Prediction and characterization of small non-coding RNAs related to secondary metabolites in Saccharopolyspora erythraea.PloS one · 2013Article
- Computational small RNA prediction in bacteria.Bioinformatics and biology insights · 2013Article
- Computational discovery and RT-PCR validation of novel Burkholderia conserved and Burkholderia pseudomallei unique sRNAs.BMC genomics · 2012Article
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2 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundThe interest in non-coding RNAs (ncRNAs) constantly rose during the past few years because of the wide spectrum of biological processes in which they are involved. This led to the discovery of numerous ncRNA genes across many species. However, for most organisms the non-coding transcriptome still remains unexplored to a great extent. Various experimental techniques for the identification of ncRNA transcripts are available, but as these methods are costly and time-consuming, there is a need for computational methods that allow the detection of functional RNAs in complete genomes in order to suggest elements for further experiments. Several programs for the genome-wide prediction of functional RNAs have been developed but most of them predict a genomic locus with no indication whether the element is transcribed or not.
resultsWe present NOCORNAc, a program for the genome-wide prediction of ncRNA transcripts in bacteria. NOCORNAc incorporates various procedures for the detection of transcriptional features which are then integrated with functional ncRNA loci to determine the transcript coordinates. We applied RNAz and NOCORNAc to the genome of Streptomyces coelicolor and detected more than 800 putative ncRNA transcripts most of them located antisense to protein-coding regions. Using a custom design microarray we profiled the expression of about 400 of these elements and found more than 300 to be transcribed, 38 of them are predicted novel ncRNA genes in intergenic regions. The expression patterns of many ncRNAs are similarly complex as those of the protein-coding genes, in particular many antisense ncRNAs show a high expression correlation with their protein-coding partner.
conclusionsWe have developed NOCORNAc, a framework that facilitates the automated characterization of functional ncRNAs. NOCORNAc increases the confidence of predicted ncRNA loci, especially if they contain transcribed ncRNAs. NOCORNAc is not restricted to intergenic regions, but it is applicable to the prediction of ncRNA transcripts in whole microbial genomes. The software as well as a user guide and example data is available at http://www.zbit.uni-tuebingen.de/pas/nocornac.htm.
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