ArticleNucleic acids research2017
FEELnc: a tool for long non-coding RNA annotation and its application to the dog transcriptome.
Article in Nucleic acids research, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 301 papers, 2 of them syntheses that pooled it.
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Who cites it
301 citing papers in PubMed, 2 syntheses or guidelines pooled it.
- A meta-analysis approach for annotation and identification of lncRNAs controlling perirenal fat deposition in suckling lambs.Animal biotechnology · 2024Pooled it
- Adaptation of the Porcine Pituitary Transcriptome, Spliceosome and Editome during Early Pregnancy.International journal of molecular sciences · 2023Pooled it
- Long non-coding RNA transcripts in crucian carp brain - annotation and expression patterns in anoxia and reoxygenation.RNA biology · 2026Article
- Large-scale genome re-annotation uncovers pathogen-specific lncRNA regulators of fungal growth and virulence.PLoS pathogens · 2026Article
- Decoding the lncRNA landscape in bovine mastitis: insights into immune regulation and gene networks underlying host response.Journal of animal science and biotechnology · 2026Article
- LncPNdeep: A long non-coding RNA classifier based on large language model with peptide and nucleotide embedding.Non-coding RNA research · 2026Article
- Integrated Survival Assessment and mRNA/miRNA Transcriptomics Reveal Heat Stress Response and Recovery Mechanisms in Cultured Razor Clam Sinonovacula constricta.Marine biotechnology (New York, N.Y.) · 2026Article
- Article
- Functional characterization of lncIMF_17214 in regulating intramuscular fat deposition of yellow-feathered broilers.Poultry science · 2026Article
- Long non-coding RNAs link DNA methylation to immune regulatory networks in bovine subclinical mastitis.Mammalian genome : official journal of the International Mammalian Genome Society · 2026Article
- Correlation of Long Non-Coding RNAs and Gene Expression in Response to Reverse Development of Turritopsis dohrnii.Marine biotechnology (New York, N.Y.) · 2026Article
- Co-Expression Network Analyses Reveal Long Non-Coding RNA Programs Associated with Trophoblast Development and Response to Zika Virus Infection in Twins Discordant for Congenital Zika Syndrome.International journal of molecular sciences · 2026Article
- Whole-transcriptome analysis reveals key transcriptional and noncoding RNA regulators of skeletal muscle satellite cell differentiation in quail.Poultry science · 2026Article
- Gestational Feed Restriction Induces Differential Expression of Novel Long Non-Coding RNAs in Offspring Skeletal Muscle.Animal genetics · 2026Article
- An integrative workflow for lncRNA orthology detection and its application to 13 evolutionarily diverse species.Nucleic acids research · 2026Article
- Identification of differentially expressed lncRNAs in different daily weight gains of Jiangquan black pigs and functional analysis of LOC100518120.BMC genomics · 2026Article
- Transcriptomic responses of red palm weevil (Coleoptera: Curculionidae) larvae to low-temperature exposure.Journal of insect science (Online) · 2026Article
- Coding and Noncoding Uterine Small Extracellular Vesicle Content Differs in the Early Stages of Pregnancies Produced by Artificial Insemination and In Vitro Fertilization in Cattle.Molecular reproduction and development · 2026Article
- Metabolic Adaptation and Potential Regulatory Mechanisms of Longissimus Dorsi-Derived Skeletal Muscle Satellite Cells from Hu Sheep Under Insulin Induction.Animals : an open access journal from MDPI · 2026Article
- Article
241 more citing papers are in PubMed but not listed here.
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Authors and funding
22 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Whole transcriptome sequencing (RNA-seq) has become a standard for cataloguing and monitoring RNA populations. One of the main bottlenecks, however, is to correctly identify the different classes of RNAs among the plethora of reconstructed transcripts, particularly those that will be translated (mRNAs) from the class of long non-coding RNAs (lncRNAs). Here, we present FEELnc (FlExible Extraction of LncRNAs), an alignment-free program that accurately annotates lncRNAs based on a Random Forest model trained with general features such as multi k-mer frequencies and relaxed open reading frames. Benchmarking versus five state-of-the-art tools shows that FEELnc achieves similar or better classification performance on GENCODE and NONCODE data sets. The program also provides specific modules that enable the user to fine-tune classification accuracy, to formalize the annotation of lncRNA classes and to identify lncRNAs even in the absence of a training set of non-coding RNAs. We used FEELnc on a real data set comprising 20 canine RNA-seq samples produced by the European LUPA consortium to substantially expand the canine genome annotation to include 10 374 novel lncRNAs and 58 640 mRNA transcripts. FEELnc moves beyond conventional coding potential classifiers by providing a standardized and complete solution for annotating lncRNAs and is freely available at https://github.com/tderrien/FEELnc.
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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.