Human Splicing Finder: an online bioinformatics tool to predict splicing signals

Human Splicing Finder: an online bioinformatics tool to predict splicing signals

2009 | François-Olivier Desmet, Dalil Hamroun, Marine Lalande, Gwenaëlle Collod-Béroud, Mireille Claustres and Christophe Béroud
Human Splicing Finder (HSF) is an online bioinformatics tool designed to predict the effects of mutations on splicing signals and identify splicing motifs in human sequences. The tool incorporates matrices for auxiliary sequence prediction, including new ones for binding sites of the 9G8 and Tra2-β Serine-Arginine proteins and the hnRNP A1 ribonucleoprotein. It also includes new Position Weight Matrices to assess the strength of 5' and 3' splice sites and branch points. HSF was evaluated using 83 intronic and 35 exonic mutations known to result in splicing defects, showing that the mutation effect was correctly predicted in almost all cases. HSF is a valuable resource for research, diagnostic, and therapeutic purposes, as well as for global studies such as the GEN2PHEN European Project and the Human Variome Project. HSF uses algorithms derived from the Universal Mutation Database (UMD) to evaluate the strength of 5' and 3' splice sites and branch points. It includes existing algorithms like RESCUE-ESE and ESE-Finder, as well as new algorithms for using available or newly created matrices. HSF includes all genes and alternative transcripts from the Ensembl human genome database, allowing the study of virtually any human sequence. The tool was tested using a set of mutations with known effects on splicing, demonstrating its ability to accurately predict the impact of mutations on splicing signals. HSF's web interface allows users to input sequences for analysis, compare mutant and wild-type sequences, and analyze multiple mutants related to the same transcript. It provides graphical displays and tables to help users understand the effects of mutations on splicing. The tool also includes specific matrices and algorithms for analyzing BP sequences or splice site motifs. HSF's algorithms were tested on various mutations affecting splicing, including those affecting 5' and 3' splice sites, branch points, and auxiliary splicing sequences. The tool correctly predicted the impact of mutations on splicing in most cases, even when complex mechanisms were involved. It was also effective in identifying cryptic splice sites created by mutations. HSF includes matrices for SR proteins and hnRNP proteins, as well as new matrices for predicting binding motifs. It uses data from experimental and computational approaches to identify ESE and ESS motifs. The tool was evaluated using a set of mutations known to affect splicing, showing its ability to accurately predict the effects of mutations on splicing signals. HSF is a valuable tool for researchers and clinicians to understand splicing events and the effects of mutations on mRNA splicing. It can also assist in designing therapeutic approaches based on splicing interference, such as exon-skipping strategies used in Duchenne Muscular Dystrophy. The tool is regularly updated to include new data from bioinformatics and experimental studies to improve predictions. HSF may also benefit global projects such as the GEN2PHEN European Project and the HumanHuman Splicing Finder (HSF) is an online bioinformatics tool designed to predict the effects of mutations on splicing signals and identify splicing motifs in human sequences. The tool incorporates matrices for auxiliary sequence prediction, including new ones for binding sites of the 9G8 and Tra2-β Serine-Arginine proteins and the hnRNP A1 ribonucleoprotein. It also includes new Position Weight Matrices to assess the strength of 5' and 3' splice sites and branch points. HSF was evaluated using 83 intronic and 35 exonic mutations known to result in splicing defects, showing that the mutation effect was correctly predicted in almost all cases. HSF is a valuable resource for research, diagnostic, and therapeutic purposes, as well as for global studies such as the GEN2PHEN European Project and the Human Variome Project. HSF uses algorithms derived from the Universal Mutation Database (UMD) to evaluate the strength of 5' and 3' splice sites and branch points. It includes existing algorithms like RESCUE-ESE and ESE-Finder, as well as new algorithms for using available or newly created matrices. HSF includes all genes and alternative transcripts from the Ensembl human genome database, allowing the study of virtually any human sequence. The tool was tested using a set of mutations with known effects on splicing, demonstrating its ability to accurately predict the impact of mutations on splicing signals. HSF's web interface allows users to input sequences for analysis, compare mutant and wild-type sequences, and analyze multiple mutants related to the same transcript. It provides graphical displays and tables to help users understand the effects of mutations on splicing. The tool also includes specific matrices and algorithms for analyzing BP sequences or splice site motifs. HSF's algorithms were tested on various mutations affecting splicing, including those affecting 5' and 3' splice sites, branch points, and auxiliary splicing sequences. The tool correctly predicted the impact of mutations on splicing in most cases, even when complex mechanisms were involved. It was also effective in identifying cryptic splice sites created by mutations. HSF includes matrices for SR proteins and hnRNP proteins, as well as new matrices for predicting binding motifs. It uses data from experimental and computational approaches to identify ESE and ESS motifs. The tool was evaluated using a set of mutations known to affect splicing, showing its ability to accurately predict the effects of mutations on splicing signals. HSF is a valuable tool for researchers and clinicians to understand splicing events and the effects of mutations on mRNA splicing. It can also assist in designing therapeutic approaches based on splicing interference, such as exon-skipping strategies used in Duchenne Muscular Dystrophy. The tool is regularly updated to include new data from bioinformatics and experimental studies to improve predictions. HSF may also benefit global projects such as the GEN2PHEN European Project and the Human
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