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Splicing defect prediction software tools | Whole-genome sequencing data analysis

In silico tools have been developed to predict variants that may have an impact on pre-mRNA splicing. The major limitation of the application of these tools to basic research and clinical practice is the difficulty in interpreting the output. Most…
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RESCUE-ESE
Web

RESCUE-ESE

Predicts which sequences have exonic splicing enhancer (ESE) activity by…

Predicts which sequences have exonic splicing enhancer (ESE) activity by statistical analysis of exon-intron and splice site composition. When large data sets of human gene sequences were used,…

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Spliceman
Web

Spliceman

Predicts how likely distant mutations around annotated splice sites were to…

Predicts how likely distant mutations around annotated splice sites were to disrupt splicing. Spliceman takes a set of DNA sequences with point mutations and returns a ranked list to predict the…

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HSF
Web

HSF Human Splicing Finder

Predicts the effects of mutations on splicing signals or to identify splicing…

Predicts the effects of mutations on splicing signals or to identify splicing motifs in any human sequence. HSF contains all available matrices for auxiliary sequence prediction as well as new ones…

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MutPred Splice
Web

MutPred Splice

A machine-learning approach for the identification of coding region…

A machine-learning approach for the identification of coding region substitutions that disrupt pre-mRNA splicing. Applying MutPred Splice to human disease-causing exonic mutations suggests that 16%…

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SKIPPY
Web

SKIPPY

A tool for the detection of exonic variants that modulate splicing. SKIPPY…

A tool for the detection of exonic variants that modulate splicing. SKIPPY allows users to input a set of exonic variants to score them for a number of features (such as changes in splicing…

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NetUTR
Web

NetUTR

Analyzes and recognizes 5' untranslated region (UTR) intron splice sites…

Analyzes and recognizes 5' untranslated region (UTR) intron splice sites in human pre-mRNA. NetUTR is able to recognize splice sites embedded in the coding parts of pre-mRNA with only a small…

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BPP
Desktop

BPP Branch Point Prediction

Estimates the affinity between the protein and the polypyrimidine tract (PPT).…

Estimates the affinity between the protein and the polypyrimidine tract (PPT). BPP can consider the co-evolution between the protein and the binding sequences. It represents the effects of…

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FSPLICE
Web

FSPLICE

Predicts potential splice sites in genomic DNA. FSPLICE allows users to search…

Predicts potential splice sites in genomic DNA. FSPLICE allows users to search for both donor and acceptor sites and to define thresholds for them independently. It also allows to search minor…

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SFmap
Web

SFmap

A web server for predicting putative splicing factor binding sites in genomic…

A web server for predicting putative splicing factor binding sites in genomic data. SFmap implements the COS(WR) algorithm, which computes similarity scores for a given regulatory motif based on…

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IntSplice
Web

IntSplice

A support vector machine (SVM) model to predict aberrant splicing because of…

A support vector machine (SVM) model to predict aberrant splicing because of intronic SNVs (Int-SNVs) at positions from Int-50 to Int-3 (Int-50:Int-3). Following an effect-size analysis of each…

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CRYP-SKIP
Web

CRYP-SKIP

A web application for 5′ and 3′ splice site prediction. CRYP-SKIP takes up…

A web application for 5′ and 3′ splice site prediction. CRYP-SKIP takes up one or more mutated alleles, each consisting of one exon and flanking intronic sequences, and provides a list of…

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ESEfinder
Web

ESEfinder

Allows for the identification of putative exonic splicing enhancers (ESEs) and…

Allows for the identification of putative exonic splicing enhancers (ESEs) and one of its most useful applications is the correct interpretation of the effects of disease-associated point mutations…

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SplicePredictor
Web

SplicePredictor

Implements Bayesian models for splice site prediction. The predictions are…

Implements Bayesian models for splice site prediction. The predictions are implicitly based on the three variables of (i) degree of matching to the splice site consensus, (ii) local compositional…

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Cosmoss
Web

Cosmoss

Provides computational biology resources that are related to the…

Provides computational biology resources that are related to the genome/transcriptome of the model plant Physcomitrella patens (Aphanoregma patens). Cosmoss is a web app that offer both the…

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NetGene2
Desktop
Web

NetGene2

A service producing neural network predictions of splice sites in human, C.…

A service producing neural network predictions of splice sites in human, C. elegans and A. thaliana DNA. The prediction output for both server and mail server consist of the prediction for both…

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SplicePort
Web

SplicePort

A versatile tool with two main functions. First, the user can perform accurate…

A versatile tool with two main functions. First, the user can perform accurate splice-site prediction on a sequence which they input to the tool, with the flexibility of exploring all the putative…

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NetPlantGene
Web

NetPlantGene

Artificial neural networks have been combined with a rule based system to…

Artificial neural networks have been combined with a rule based system to predict intron splice sites in the dicot plant Arabidopsis thaliana. A two step prediction scheme, where a global prediction…

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SROOGLE
Desktop
Web

SROOGLE Splicing RegulatiOn Online GraphicaL Engine

Makes splicing signal sequence and scoring data available to the biologist in…

Makes splicing signal sequence and scoring data available to the biologist in an integrated, visual, easily interpretable, and user-friendly format. SROOGLE's input consists of the sequence of…

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GeneSplicer
Desktop
Web

GeneSplicer

A flexible system for detecting splice sites in the genomic DNA of various…

A flexible system for detecting splice sites in the genomic DNA of various eukaryotes. The system has been trained and tested successfully on Plasmodium falciparum (malaria), Arabidopsis thaliana,…

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NetAspGene
Web

NetAspGene

Predicts splice site of the genus Aspergillus. NetAspGene can be combined with…

Predicts splice site of the genus Aspergillus. NetAspGene can be combined with a gene finder to develop better annotation for Aspergillus genes. It will be very helpful for the researchers who are…

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AASsites
Web

AASsites

An automated bioinformatics pipeline to analyse SNP containing DNA sequences…

An automated bioinformatics pipeline to analyse SNP containing DNA sequences mainly for finding SNPs which cause a change in the splicing pattern. AASsites first determines the position of the SNP.…

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SpliceView
Web

SpliceView

A web application for functional site analysis. SpliceView is based on four…

A web application for functional site analysis. SpliceView is based on four main assumptions: each variation of nucleotide composition makes a different contribution to the overall binding free…

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MaxEntScan
Desktop
Web

MaxEntScan

Scores Human 5' splice sites. MaxEntScan is based on the approach for…

Scores Human 5' splice sites. MaxEntScan is based on the approach for modeling the sequences of short sequence motifs such as those involved in RNA splicing which simultaneously accounts for…

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NNSplice
Web

NNSplice

An improved splice site predictor for the genefinding program Genie. The…

An improved splice site predictor for the genefinding program Genie. The training and test sets of human and Drosophila melanogaster splice sites are available to the community for testing splice…

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PESX
Web

PESX Putative Exonic Splicing Enhancers/Silencers

A computational approach to identify exonic splicing enhancers (ESEs) and…

A computational approach to identify exonic splicing enhancers (ESEs) and exonic splicing silencers (ESSs) associated with constitutively spliced exons. The large number of effective sequences…

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