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

TitleIn silico tools for splicing defect prediction: a survey from the viewpoint of end users.
Publication TypeJournal Article
Year of Publication2014
AuthorsJian, X, Boerwinkle, E, Liu, X
JournalGenet Med
Volume16
Issue7
Pagination497-503
Date Published2014 Jul
ISSN1530-0366
KeywordsComputational Biology, Computer Simulation, Genetic Variation, Humans, RNA Precursors, RNA Splicing, Software
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.

DOI10.1038/gim.2013.176
Alternate JournalGenet. Med.
PubMed ID24263461
PubMed Central IDPMC4029872
Grant ListP50 GM065509 / GM / NIGMS NIH HHS / United States
RC2 HL102419 / HL / NHLBI NIH HHS / United States
P50GM065509 / GM / NIGMS NIH HHS / United States
RC2-HL102419 / HL / NHLBI NIH HHS / United States