ArticleBMC bioinformatics2014
PLEK: a tool for predicting long non-coding RNAs and messenger RNAs based on an improved k-mer scheme.
Article in BMC bioinformatics, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 435 papers, 1 of them a synthesis that pooled it.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
435 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Adaptation of the Porcine Pituitary Transcriptome, Spliceosome and Editome during Early Pregnancy.International journal of molecular sciences · 2023Pooled it
- HyLnc: a hybrid deep learning and feature-based approach for long non-coding RNA prediction.RNA biology · 2026Article
- A copy-number variation generates a long-noncoding RNA that enhances ClBige1b expression to suppress cell expansion and seed growth in watermelon.Plant communications · 2026Article
- LncPNdeep: A long non-coding RNA classifier based on large language model with peptide and nucleotide embedding.Non-coding RNA research · 2026Article
- Population Genomics Refines Population Structure and Individual Stock Assignment in Atlantic and Mediterranean Swordfish (International journal of molecular sciences · 2026Article
- Deciphering differential mRNA and lncRNA expression profiles in response to PEG simulated drought stress in cucumber (Cucumis sativus L.).Journal, genetic engineering & biotechnology · 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
- The Landscape of Long Non-Coding RNAs Provides Insights Into the Domestication and Improvement of Pear Fruit.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Retina-specific long non-coding RNAs associated with inherited retinal disease genes.Cellular and molecular life sciences : CMLS · 2026Article
- Elucidation of sugar metabolic profiles and transcriptional regulatory networks during the developmental stages of sweet corn kernels.iScience · 2026Article
- Genome-Wide Characterization of Long Non-Coding RNAs Identifies Candidate Regulatory Networks During Modern Maize Breeding.Plants (Basel, Switzerland) · 2026Article
- Comprehensive lincRNA Transcriptome in Acute Myeloid Leukemia: Integrating Known and Newly Identified lincRNAs Across Pediatric and Adult Cohorts.Non-coding RNA · 2026Article
- Reference-guided genome assembly of long non-coding rna transcripts reveals target genes associated with Crohn's disease.Scientific reports · 2026Article
- Transcriptome analysis revealed lncRNA-mRNA modules responsive to low temperature stress in Qingke.BMC genomics · 2026Article
- WFDC21P is essential for G3BP1-mediated RIG-I activation and antitumor immunity in triple-negative breast cancer.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- Machine and Deep Learning Reveal Sequence Determinants Encoding Bivalent Histone Modifications.Communications biology · 2026Article
- Comparative transcriptome analysis reveals underlying aggressiveness mechanisms of Sclerotinia sclerotiorum infecting Brassica juncea.Archives of microbiology · 2026Article
- Characterization of the full-length transcriptome of female Eucoleus annulatus and comparative transcriptomic analysis of its head, middle, and tail body sections.Parasites & vectors · 2026Article
- Whole transcriptome sequencing of different hair types in inner Mongolian cashmere goats.BMC genomics · 2026Article
- Full-length transcriptome sequencing analysis and characterization of MADS-box genes in Rhododendron fortunei.BMC plant biology · 2026Article
375 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundHigh-throughput transcriptome sequencing (RNA-seq) technology promises to discover novel protein-coding and non-coding transcripts, particularly the identification of long non-coding RNAs (lncRNAs) from de novo sequencing data. This requires tools that are not restricted by prior gene annotations, genomic sequences and high-quality sequencing.
resultsWe present an alignment-free tool called PLEK (predictor of long non-coding RNAs and messenger RNAs based on an improved k-mer scheme), which uses a computational pipeline based on an improved k-mer scheme and a support vector machine (SVM) algorithm to distinguish lncRNAs from messenger RNAs (mRNAs), in the absence of genomic sequences or annotations. The performance of PLEK was evaluated on well-annotated mRNA and lncRNA transcripts. 10-fold cross-validation tests on human RefSeq mRNAs and GENCODE lncRNAs indicated that our tool could achieve accuracy of up to 95.6%. We demonstrated the utility of PLEK on transcripts from other vertebrates using the model built from human datasets. PLEK attained >90% accuracy on most of these datasets. PLEK also performed well using a simulated dataset and two real de novo assembled transcriptome datasets (sequenced by PacBio and 454 platforms) with relatively high indel sequencing errors. In addition, PLEK is approximately eightfold faster than a newly developed alignment-free tool, named Coding-Non-Coding Index (CNCI), and 244 times faster than the most popular alignment-based tool, Coding Potential Calculator (CPC), in a single-threading running manner.
conclusionsPLEK is an efficient alignment-free computational tool to distinguish lncRNAs from mRNAs in RNA-seq transcriptomes of species lacking reference genomes. PLEK is especially suitable for PacBio or 454 sequencing data and large-scale transcriptome data. Its open-source software can be freely downloaded from https://sourceforge.net/projects/plek/files/.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
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.