Spliceogen

Spliceogen identifies genome-scale splice-altering variants by integrating predictions from MaxEntScan, GeneSplicer, ESRseq, and Branchpointer to detect creation or disruption of cis-splicing motifs.

Key Features:

• Integrated splice motif prediction models: Combines predictions from MaxEntScan, GeneSplicer, ESRseq, and Branchpointer for splice motif assessment.
• Input formats: Accepts VCF (Variant Call Format) and BED file inputs.
• Variant types supported: Analyzes single nucleotide variants (SNVs) and insertions/deletions (indels).
• Genome-scale motif discovery: Identifies variants that create or disrupt cis-splicing motifs across the genome.
• Gencode multi-exon transcript coverage: Provides prediction scores for all possible SNVs at every genomic position within Gencode-annotated multi-exon transcripts.
• Scalability: Designed to process large genomic datasets for genome-scale analyses.

Scientific Applications:

• Genetic disease research: Supports identification of splice-altering variants that may contribute to Mendelian and complex diseases.
• Personalized medicine: Enables assessment of variant impacts on splicing for variant interpretation and patient-specific analyses.
• Evolutionary biology: Facilitates study of splicing variation and its evolutionary consequences across genomes.
• Genome-wide splicing studies: Supports large-scale analyses of how variants alter splicing motifs within annotated transcripts.

Methodology:

Integrates prediction outputs from MaxEntScan, GeneSplicer, ESRseq, and Branchpointer; accepts VCF and BED inputs and analyzes SNVs and indels; generates prediction scores for all possible SNVs at every genomic position within Gencode-annotated multi-exon transcripts and reports variants that create or disrupt cis-splicing motifs.