ArticleNucleic acids research2019
CNIT: a fast and accurate web tool for identifying protein-coding and long non-coding transcripts based on intrinsic sequence composition.
Article in Nucleic acids research, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 76 papers.
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Who cites it
76 citing papers in PubMed.
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- The chloroplast-targeted long noncoding RNA CHLORELLA mediates chloroplast functional transition across leaf ageing via anterograde signalling.Nature plants · 2025Article
- Strict retroelement regulation is frequently lost following cancer transformation and generates a promising reservoir of cancer biomarkers.Mobile DNA · 2025Article
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- Molecular and expression analyses indicate the role of fusion transcripts in mediating abiotic stress responses in chickpea.Frontiers in plant science · 2025Article
- TSS-Captur: a user-friendly pipeline for characterizing unclassified RNA transcripts.NAR genomics and bioinformatics · 2024Article
- Long non-coding RNA-encoded micropeptides: functions, mechanisms and implications.Cell death discovery · 2024Review
- Transcriptomic analyses of differentially expressed human genes, micro RNAs and long-non-coding RNAs in severe, symptomatic and asymptomatic malaria infection.Scientific reports · 2024Article
- Long non-coding RNAs expression and regulation across different brain regions in primates.Scientific data · 2024Article
- RUNX1-IT1 acts as a scaffold of STAT1 and NuRD complex to promote ROS-mediated NF-κB activation and ovarian cancer progression.Oncogene · 2024Article
- Disparate macrophage responses are linked to infection outcome of Hantan virus in humans or rodents.Nature communications · 2024Article
- A task-specific encoding algorithm for RNAs and RNA-associated interactions based on convolutional autoencoder.Nucleic acids research · 2023Article
- Long noncoding RNA study: Genome-wide approaches.Genes & diseases · 2023Review
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- Analysis of lncRNAs inNon-coding RNA · 2023Article
- IRSOM2: a web server for predicting bifunctional RNAs.Nucleic acids research · 2023Article
16 more citing papers are in PubMed but not listed here.
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Authors and funding
12 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
As more and more high-throughput data has been produced by next-generation sequencing, it is still a challenge to classify RNA transcripts into protein-coding or non-coding, especially for poorly annotated species. We upgraded our original coding potential calculator, CNCI (Coding-Non-Coding Index), to CNIT (Coding-Non-Coding Identifying Tool), which provides faster and more accurate evaluation of the coding ability of RNA transcripts. CNIT runs ∼200 times faster than CNCI and exhibits more accuracy compared with CNCI (0.98 versus 0.94 for human, 0.95 versus 0.93 for mouse, 0.93 versus 0.92 for zebrafish, 0.93 versus 0.92 for fruit fly, 0.92 versus 0.88 for worm, and 0.98 versus 0.85 for Arabidopsis transcripts). Moreover, the AUC values of 11 animal species and 27 plant species showed that CNIT was capable of obtaining relatively accurate identification results for almost all eukaryotic transcripts. In addition, a mobile-friendly web server is now freely available at http://cnit.noncode.org/CNIT.
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