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Cited by 146RNA Research and SplicingGenomics and Rare DiseasesRNA and protein synthesis mechanisms

In silico tools for splicing defect prediction: a survey from the viewpoint of end users

Open access
Jian, Xueqiu, Boerwinkle, Eric, Liu, Xiaoming·2014·Genetics in Medicine
DOI 10.1038/gim.2013.176PMC PMC4029872
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Abstract

RNA splicing is the process during which introns are excised and exons are spliced. The precise recognition of splicing signals is critical to this process, and mutations affecting splicing comprise a considerable proportion of genetic disease etiology. Analysis of RNA samples from the patient is the most straightforward and reliable method to detect splicing defects. However, currently, the technical limitation prohibits its use in routine clinical practice. In silico tools that predict potential consequences of splicing mutations may be useful in daily diagnostic activities. In this review, we provide medical geneticists with some basic insights into some of the most popular in silico tools for splicing defect prediction, from the viewpoint of end users. Bioinformaticians in relevant areas who are working on huge data sets may also benefit from this review. Specifically, we focus on those tools whose primary goal is to predict the impact of mutations within the 5' and 3' splicing consensus regions: the algorithms used by different tools as well as their major advantages and disadvantages are briefly introduced; the formats of their input and output are summarized; and the interpretation, evaluation, and prospection are also discussed.

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Authors
Jian, X., Boerwinkle, E., & Liu, X.
Affiliations
  • The University of Texas Health Science Center at Houston (US)
  • Baylor College of Medicine (US)
Corresponding author
Liu, Xiaoming
ORCID
Venue
Genetics in Medicine
Publisher
Elsevier BV
Published
2014-07
Volume
16
Issue
7
Pages
497-503
ISSN
1098-3600 (ISSN-L)
DOI
10.1038/gim.2013.176
PMC
PMC4029872
OpenAlex
W1976579581
Cited by
146
References
41
Citations by year
2026: 4 · 2025: 7 · 2024: 10 · 2023: 10 · 2022: 19 · 2021: 24 · 2020: 13 · 2019: 11 · 2018: 16 · 2017: 13 · 2016: 11 · 2015: 6 · 2014: 2
FWCI
0.60
Type
journal article
Language
en
Open access
Licence
Locations
  • Genetics in Medicine (publishedVersion)
  • PubMed (publishedVersion)
  • Europe PMC (PubMed Central) (acceptedVersion)
  • PubMed Central (acceptedVersion)
Funders
  • National Institutes of Health (5p50gm065509-10)
  • National Heart, Lung, and Blood Institute (RC2HL102419)
  • National Institute of General Medical Sciences (P50-GM065509)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA Research and Splicing
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genomics and Rare Diseases
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA and protein synthesis mechanisms
Keywords
RNA splicing, splicing mutation, 5' splice site, 3' splice site, in silico prediction tools, end-user evaluation, tool comparison
MeSH terms
Computer Simulation, Humans, RNA Precursors, RNA Splicing, Software, Genetic Variation, Computational Biology

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