SplicePort

SplicePort predicts splice sites in human and other mammalian nucleotide sequences and provides feature-based analysis to support studies of gene expression and alternative splicing.

Key Features:

• Splice-Site Prediction: Predicts donor and acceptor splice sites in nucleotide sequences using a catalog of optimized sequence-derived features.
• Feature Catalog: Maintains a comprehensive catalog of sequence-derived features optimized for human splice sites and applicable to other mammals.
• Feature Visualization: Generates visual representations of selected feature subsets or the complete feature set to indicate feature contributions to classification.
• Feature Clustering and Analysis: Clusters features and produces frequency-plot WebLogos for each cluster to reveal sequence motifs and splice-site signals.
• Search and Rank Features: Enables search and ranking of features to prioritize features based on their contribution to splice-site classification.

Scientific Applications:

• Gene expression and alternative splicing studies: Supports analysis of gene expression regulation and identification of alternative splicing events through splice-site prediction and feature analysis.
• Variant interpretation and genetic disorder research: Assists interpretation of sequence variants affecting splice sites and investigation of genetic disorders involving splicing defects.
• Motif discovery and validation: Facilitates discovery and validation of splice-site signals and sequence motifs via feature clustering and WebLogos.

Methodology:

Performs splice-site prediction on nucleotide sequences using a catalog of sequence-derived features; supports feature search and ranking, feature clustering, generation of frequency-plot WebLogos, and visualization of feature subsets.