SFmap

SFmap predicts potential splicing factor (SF) binding sites within genomic sequences to support analysis of alternative splicing (AS).

Key Features:

• COS(WR) Algorithm Implementation: SFmap employs the COS(WR) algorithm to calculate motif similarity scores using local sequence environment and evolutionary conservation.
• Motif search and scoring: The software searches input sequences for significant hits of binding motifs and evaluates their similarity scores.
• Motif sources: SFmap can use motifs stored in an internal database or motifs defined by users.
• Input formats: The tool accepts human genomic sequences and lists of sequences in FASTA format.

Scientific Applications:

• Alternative splicing regulation: Identification of SF binding sites to investigate regulatory mechanisms underlying AS.
• Functional impact on protein diversity: Exploration of how SF binding influences AS events that contribute to protein diversity.
• Genomics and bioinformatics analyses: Provision of predicted SF binding sites for studies in genomics, molecular biology, and bioinformatics.

Methodology:

The COS(WR) algorithm integrates sequence context and evolutionary conservation to compute motif similarity scores, SFmap searches sequences for significant motif hits, and it accepts motifs from an internal database or user-defined sets.