ArticleGenomics, proteomics & bioinformatics2012
Searching for non-coding RNAs in genomic sequences using ncRNAscout.
Article in Genomics, proteomics & bioinformatics, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 5 papers.
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Who cites it
5 citing papers in PubMed, 9 citations in OpenAlex.
- mSRFR: a machine learning model using microalgal signature features for ncRNA classification.BioData mining · 2022Article
- Distribution of ncRNAs expression across hypothalamic-pituitary-gonadal axis in Capra hircus.BMC genomics · 2018Article
- LncRNApred: Classification of Long Non-Coding RNAs and Protein-Coding Transcripts by the Ensemble Algorithm with a New Hybrid Feature.PloS one · 2016Article
- Identification of non-coding RNAs with a new composite feature in the Hybrid Random Forest Ensemble algorithm.Nucleic acids research · 2014Article
- Computational Detection of piRNA in Human Using Support Vector Machine.Avicenna journal of medical biotechnologyArticle
Corrections and comments
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Authors and funding
4 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Recently non-coding RNA (ncRNA) genes have been found to serve many important functions in the cell such as regulation of gene expression at the transcriptional level. Potentially there are more ncRNA molecules yet to be found and their possible functions are to be revealed. The discovery of ncRNAs is a difficult task because they lack sequence indicators such as the start and stop codons displayed by protein-coding RNAs. Current methods utilize either sequence motifs or structural parameters to detect novel ncRNAs within genomes. Here, we present an ab initio ncRNA finder, named ncRNAscout, by utilizing both sequence motifs and structural parameters. Specifically, our method has three components: (i) a measure of the frequency of a sequence, (ii) a measure of the structural stability of a sequence contained in a t-score, and (iii) a measure of the frequency of certain patterns within a sequence that may indicate the presence of ncRNA. Experimental results show that, given a genome and a set of known ncRNAs, our method is able to accurately identify and locate a significant number of ncRNA sequences in the genome. The ncRNAscout tool is available for downloading at http://bioinformatics.njit.edu/ncRNAscout.
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Registered trials
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