• Home page
    • User registration
    • Login
  • Products
    • Gensearch
    • PMCR
    • Mutalyzer support
    • GensearchHIV
    • GensearchNGS
    • GensearchVET
    • GensearchGT
    • eMLPA
    • P3RED: Crédit d'Impôt Recherche
    • Genetic Variant Interpretation Tool (ACMG/AMP) - French
    • Genetic Variant Interpretation Tool (ACMG/AMP) - Czech
  • Links
    • LSDB list
    • LSDB software
    • Splice prediction tools
    • Other prediction tools
    • Documents and guidelines
    • HIV tools
    • NGS tools
  • R&D
    • capHIV
    • Gen2Phen FP7
    • NMDchip FP7
  • Contact us
    • Privacy policy

Splice prediction tools

You can find here a collection of various splice prediction tools. You might want to check out as well our documents and guideline section as it contains reports about the use of those tools. You are also welcome to propose to add tools to below list, just contact us!

  • Hits: 15157
    Web Link Fruit Fly Splice Predictor

    Fruit fly and human splice predictor.
    Directly callable from our sequencing software Gensearch.

  • Hits: 34817
    Web Link Human Splicing Finder

    In order to better understand intronic and exonic mutations leading to splicing defects, we decided to create the Human Splicing Finder website. This tool is aimed to help study of the pre-mRNA splicing. 

    To calculate the consensus values of potential splice sites and search for branch points, new algorithms were developed. Furthermore, we have integrated all available matrices to identify exonic and intronic motifs, as well as new matrices to identify hnRNP A1, Tra2-β and 9G8.

  • Hits: 12499
    Web Link RegRNA: A Regulatory RNA Motifs and Elements Finder

    Integrated web server, namely RegRNA, to identify the homologs of Regulatory RNA motifs and elements against an input mRNA sequence. Both sequence homologs or structural homologs of regulatory RNA motifs can be identified. The regulatory RNA motifs supported in RegRNA are categorized into several classes:

    • Motifs in mRNA 5'-UTR and 3'-UTR. 
    • Motifs involved in mRNA splicing.
    • Motifs involved in transcriptional regulation. 
    • Other motifs in mRNA, such as riboswitches. 
    • Prediction of the splice sites, such as splicing donor/acceptor sites.
    • RNA structural features, such as inverted repeat.
    • miRNA target sites.
  • Hits: 9885
    Web Link ESEfinder: Exonic Splicing Enhancers finder

    Analyzes the exonic sequence to find the presence of Exonic Splicing Enhancer Elements

  • Hits: 14185
    Web Link MIT splice predictor

    GENSCAN Web Server at MIT: identification of complete gene structures in genomic DNA. Directly callable from ou sequencing software Gensearch.

  • Hits: 18762
    Web Link GeneSplicer

    A fast, 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, human, Drosophila, and rice . Training data sets for human and Arabidopsis thaliana are included. Use the GeneSplicer Web Interface to run GeneSplicer directly, or see below for instructions on downloading the complete system including source code . 

  • Hits: 14242
    Web Link Splice Predictor (DK)

    The NetGene2 server is a service producing neural network predictions of splice sites in human, C. elegans and A. thaliana DNA.

  • Hits: 11118
    Web Link Alternative Splice Site Predictor (ASSP)

    ASSP predicts putative alternative exon isoform, cryptic, and constitutive splice sites of internal (coding) exons. Skipped splice sites are not differentiated from constitutive sites. Non-canonical splice sites are not detected. Alternative splicing is predicted based on the DNA/RNA sequence information only. For splice site prediction within a sequence putative splice sites are preprocessed using position specific score matrices.

  • Hits: 10988
    Web Link SplicePort: An Interactive Splice Site Analysis Tool

    SplicePort is a web-based tool for splice-site analysis that allows the user to make splice-site predictions for submitted sequences. In addition, the user can also browse the rich catalog of features that underlies these predictions, and which we (the authors) have found capable of providing high classification accuracy on human splice sites. Feature selection is optimized for human splice sites, but the selected features are likely to be predictive for other mammals as well.

    Publication

  • Hits: 4801
    Web Link MaxEntScan: predicting splice sites using 'Maximum Entropy Principle'

    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 non-adjacent as well as adjacent dependencies between positions. This method is based on the 'Maximum Entropy Principle' and generalizes most previous probabilistic models of sequence motifs such as weight matrix models and inhomogeneous Markov models.

  • Hits: 4353
    Web Link EX-SKIP: comparing ESE/ESS profile of a wild-type and a mutated allele

    EX-SKIP is simple utility that compares the ESE/ESS profile of a wild-type and a mutated allele to quickly determine which exonic variant has the highest chance to skip this exon. It calculates the total number of ESSs, ESEs and their ratio. Specifically, it computes the number of RESCUE-ESEs (Fairbrother 2004; Fairbrother 2002), FAS-ESSs (Wang 2004), PESEs/PESSs (Zhang 2004), neighbourhood inference (Stadler 2006) and EIE/IIEs (Zhang 2008) for each segment.

  • Hits: 3532
    Web Link RESCUE-ESE: online tool for identifying candidate ESEs in vertebrate exons

    Specific short oligonucleotide sequences that enhance pre-mRNA splicing when present in exons, termed exonic splicing enhancers (ESEs), play important roles in constitutive and alternative splicing (ESE References). A hybrid computational/experimental method, RESCUE-ESE, was recently developed for identifying sequences with ESE activity. In this approach, specific hexanucleotide sequences are identified as candidate ESEs on the basis that they have both significantly higher frequency of occurrence in exons than in introns and also significantly higher frequency in exons with weak (non-consensus) splice sites than in exons with strong (consensus) splice sites. Representative hexamers from ten different classes of candidate ESEs, together with 6 or 7 bases of flanking sequence context on each side, were introduced into a weak (poorly spliced) exon in a splicing reporter construct. These reporter minigenes were then transfected into cultured cells, where they are transcribed and spliced, and the relative level of inclusion of the test exon was assayed by quantitative (radio-labeled) RT-PCR. Point mutants of these sequences were also analyzed to confirm the precise motifs responsible for ESE activity.

Copyrights 2012 Phenosystems SA