ReviewCurrent genomics2017
Comparison of Alternative Splicing Junction Detection Tools Using RNA-Seq Data.
Review in Current genomics, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
What it found
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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
19 citing papers in PubMed.
- Detection of alternative splicing: deep sequencing or deep learning?Briefings in bioinformatics · 2026Article
- A novel splicing graph allows a direct comparison between exon-based and splice junction-based approaches to alternative splicing detection.Briefings in bioinformatics · 2025Article
- Identification of diagnostic candidates in Mendelian disorders using an RNA sequencing-centric approach.Genome medicine · 2024Article
- Identification of Splice Variants and Isoforms in Transcriptomics and Proteomics.Annual review of biomedical data science · 2023Review
- Allele-specific quantification of human leukocyte antigen transcript isoforms by nanopore sequencing.Frontiers in immunology · 2023Article
- Role of Epitranscriptomic and Epigenetic Modifications during the Lytic and Latent Phases of Herpesvirus Infections.Microorganisms · 2022Review
- Splice variants denote differences between a cancer stem cell side population of EWSR1‑ERG‑based Ewing sarcoma cells, its main population and EWSR1‑FLI‑based cells.International journal of molecular medicine · 2022Article
- Splice Junction Identification using Long Short-Term Memory Neural Networks.Current genomics · 2021Article
- Review
- Alternative RNA splicing in stem cells and cancer stem cells: Importance of transcript-based expression analysis.World journal of stem cells · 2021Review
- Alternative splicing dynamics and evolutionary divergence during embryogenesis in wheat species.Plant biotechnology journal · 2021Article
- Computational comparison of common event-based differential splicing tools: practical considerations for laboratory researchers.BMC bioinformatics · 2021Article
- Genome-wide discovery of natural variation in pre-mRNA splicing and prioritising causal alternative splicing to salt stress response in rice.The New phytologist · 2021Article
- Comprehensive Comparison of Amnion Stromal Cells and Chorion Stromal Cells by RNA-Seq.International journal of molecular sciences · 2021Article
- Review
- RBM20 Regulates CaV1.2 Surface Expression by Promoting Exon 9* Inclusion ofInternational journal of molecular sciences · 2019Article
- Altered RNA Processing in Cancer Pathogenesis and Therapy.Cancer discovery · 2019Review
- Visualization and analysis of RNA-Seq assembly graphs.Nucleic acids research · 2019Article
- Event Analysis: Using Transcript Events To Improve Estimates of Abundance in RNA-seq Data.G3 (Bethesda, Md.) · 2018Article
Corrections and comments
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Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundAlternative splicing (AS) is a posttranscriptional process that produces differ-ent transcripts from the same gene and is important to produce diverse protein products in response to environmental stimuli. AS occurs at specific sites on the mRNA sequence, some of which have been de-fined. Multiple bioinformatics tools have been developed to detect AS from experimental data.
objectivesThe goal of this review is to help researchers use specific tools to aid their research and to develop new AS detection tools based on these previously established tools.
methodWe selected 15 AS detection tools that were recently published; we classified and delineated them on several aspects. Also, a performance comparison of these tools with the same starting input was conducted.
resultWe reviewed the following categorized features of the tools: Publication information, working principles, generic and distinct workflows, running platform, input data requirement, sequencing depth dependency, reads mapped to multiple locations, isoform annotation basis, precise detected AS types, and performance benchmarks.
conclusionThrough comparisons of these tools, we provide a panorama of the advantages and short-comings of each tool and their scopes of application.
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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.