ArticleBMC genomics2010
POLYAR, a new computer program for prediction of poly(A) sites in human sequences.
Article in BMC genomics, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 27 papers.
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Who cites it
27 citing papers in PubMed, 54 citations in OpenAlex.
- A Survey on Methods for Predicting Polyadenylation Sites from DNA Sequences, Bulk RNA-seq, and Single-cell RNA-seq.Genomics, proteomics & bioinformatics · 2023Review
- CRISPRs in the human genome are differentially expressed between malignant and normal adjacent to tumor tissue.Communications biology · 2022Article
- Intron mutations and early transcription termination in Duchenne and Becker muscular dystrophy.Human mutation · 2022Article
- From shallow to deep: some lessons learned from application of machine learning for recognition of functional genomic elements in human genome.Human genomics · 2022Review
- Detecting and Profiling Endogenous RNA G-Quadruplexes in the Human Transcriptome.International journal of molecular sciences · 2021Article
- Aptardi predicts polyadenylation sites in sample-specific transcriptomes using high-throughput RNA sequencing and DNA sequence.Nature communications · 2021Article
- Advances in the Bioinformatics Knowledge of mRNA Polyadenylation in Baculovirus Genes.Viruses · 2020Review
- DeepPASTA: deep neural network based polyadenylation site analysis.Bioinformatics (Oxford, England) · 2019Article
- Sequence determinants of polyadenylation-mediated regulation.Genome research · 2019Article
- DeeReCT-PolyA: a robust and generic deep learning method for PAS identification.Bioinformatics (Oxford, England) · 2019Article
- Cross-Regulation between TDP-43 and Paraspeckles Promotes Pluripotency-Differentiation Transition.Molecular cell · 2019Article
- Inference of the human polyadenylation code.Bioinformatics (Oxford, England) · 2018Article
- QAPA: a new method for the systematic analysis of alternative polyadenylation from RNA-seq data.Genome biology · 2018Article
- XBSeq2: a fast and accurate quantification of differential expression and differential polyadenylation.BMC bioinformatics · 2017Article
- Omni-PolyA: a method and tool for accurate recognition of Poly(A) signals in human genomic DNA.BMC genomics · 2017Article
- High-Resolution RNA Maps Suggest Common Principles of Splicing and Polyadenylation Regulation by TDP-43.Cell reports · 2017Article
- Poly(A) code analyses reveal key determinants for tissue-specific mRNA alternative polyadenylation.RNA (New York, N.Y.) · 2016Article
- Motif types, motif locations and base composition patterns around the RNA polyadenylation site in microorganisms, plants and animals.BMC evolutionary biology · 2014Article
- IB4-binding sensory neurons in the adult rat express a novel 3' UTR-extended isoform of CaMK4 that is associated with its localization to axons.The Journal of comparative neurology · 2014Article
- Genome-wide identification and predictive modeling of tissue-specific alternative polyadenylation.Bioinformatics (Oxford, England) · 2013Article
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Authors and funding
5 authors at 2 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundmRNA polyadenylation is an essential step of pre-mRNA processing in eukaryotes. Accurate prediction of the pre-mRNA 3'-end cleavage/polyadenylation sites is important for defining the gene boundaries and understanding gene expression mechanisms.
results28761 human mapped poly(A) sites have been classified into three classes containing different known forms of polyadenylation signal (PAS) or none of them (PAS-strong, PAS-weak and PAS-less, respectively) and a new computer program POLYAR for the prediction of poly(A) sites of each class was developed. In comparison with polya_svm (till date the most accurate computer program for prediction of poly(A) sites) while searching for PAS-strong poly(A) sites in human sequences, POLYAR had a significantly higher prediction sensitivity (80.8% versus 65.7%) and specificity (66.4% versus 51.7%) However, when a similar sort of search was conducted for PAS-weak and PAS-less poly(A) sites, both programs had a very low prediction accuracy, which indicates that our knowledge about factors involved in the determination of the poly(A) sites is not sufficient to identify such polyadenylation regions.
conclusionsWe present a new classification of polyadenylation sites into three classes and a novel computer program POLYAR for prediction of poly(A) sites/regions of each of the class. In tests, POLYAR shows high accuracy of prediction of the PAS-strong poly(A) sites, though this program's efficiency in searching for PAS-weak and PAS-less poly(A) sites is not very high but is comparable to other available programs. These findings suggest that additional characteristics of such poly(A) sites remain to be elucidated. POLYAR program with a stand-alone version for downloading is available at http://cub.comsats.edu.pk/polyapredict.htm.
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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.