![]() Cis-acting elements contain the 5′ splice site (junction between an exon and an intron), the 3′ splice site (junction between an intron and an exon), the branch point (tens of nucleotides upstream of the 3′ splice site), exonic splicing enhancers (ESEs), intronic splicing enhancers, exonic splicing silencers, and intronic splicing silencers. The completion and regulation of splicing lean on the complicated biochemical reactions between the nucleotide sequences ( cis-acting elements) and different proteins binding to them ( trans-acting elements). ![]() 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. Bioinformaticians in relevant areas who are working on huge data sets may also benefit from this review. 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. In silico tools that predict potential consequences of splicing mutations may be useful in daily diagnostic activities. However, currently, the technical limitation prohibits its use in routine clinical practice. Analysis of RNA samples from the patient is the most straightforward and reliable method to detect splicing defects. The precise recognition of splicing signals is critical to this process, and mutations affecting splicing comprise a considerable proportion of genetic disease etiology. RNA splicing is the process during which introns are excised and exons are spliced.
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