jaspar-database

To scan DNA for transcription factor binding sites, query JASPAR motif profiles via the REST API, convert the PFM to a PWM, and perform strand-aware sequence scanning with configurable thresholds to identify predicted binding hits.

Yes, GWAS variant impact assessment compares reference versus alternative DNA sequences using PWM-based scoring to determine how sequence variants disrupt or create regulatory transcription factor binding sites.

PWM scoring converts a JASPAR position frequency matrix into a log-odds matrix with pseudocount handling, then scans both DNA strands to calculate binding probabilities and identify transcription factor hits above configurable thresholds.

You can search JASPAR transcription factor matrices by name, species, class, family, and collection using the REST API to retrieve specific PFMs for ChIP-seq peak motif matching and regulatory interpretation.

Yes, JASPAR PWM scanning supports regulatory genomics tasks including motif discovery, enrichment analysis, and promoter or enhancer interpretation by identifying transcription factor binding sites across DNA sequences.

Pseudocount handling is required during PFM to PWM conversion to prevent zero-probability positions from causing infinite log-odds scores, ensuring accurate strand-aware transcription factor binding site predictions across DNA sequences.