ArticleRNA (New York, N.Y.)2011
RNAcode: robust discrimination of coding and noncoding regions in comparative sequence data.
Article in RNA (New York, N.Y.), 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 122 papers.
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Who cites it
122 citing papers in PubMed.
- Dissecting the genetics of the human transcriptome identifies novel trait-related trans-eQTLs and corroborates the regulatory relevance of non-protein coding loci†.Human molecular genetics · 2015Trial
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- The Cryptic Bacterial Microproteome.bioRxiv : the preprint server for biology · 2024Article
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- Computational exploration of the global microbiome for antibiotic discovery.bioRxiv : the preprint server for biology · 2023Article
- Tailored machine learning models for functional RNA detection in genome-wide screens.NAR genomics and bioinformatics · 2023Article
- RNAcode_Web - Convenient identification of evolutionary conserved protein coding regions.Journal of integrative bioinformatics · 2023Article
- CodingDiv: analyzing SNP-level microdiversity to discriminate between coding and noncoding regions in viral genomes.Bioinformatics (Oxford, England) · 2023Article
62 more citing papers are in PubMed but not listed here.
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Authors and funding
8 authors.
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Abstract
With the availability of genome-wide transcription data and massive comparative sequencing, the discrimination of coding from noncoding RNAs and the assessment of coding potential in evolutionarily conserved regions arose as a core analysis task. Here we present RNAcode, a program to detect coding regions in multiple sequence alignments that is optimized for emerging applications not covered by current protein gene-finding software. Our algorithm combines information from nucleotide substitution and gap patterns in a unified framework and also deals with real-life issues such as alignment and sequencing errors. It uses an explicit statistical model with no machine learning component and can therefore be applied "out of the box," without any training, to data from all domains of life. We describe the RNAcode method and apply it in combination with mass spectrometry experiments to predict and confirm seven novel short peptides in Escherichia coli and to analyze the coding potential of RNAs previously annotated as "noncoding." RNAcode is open source software and available for all major platforms at http://wash.github.com/rnacode.
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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.