alterlab-jaspar

To scan DNA sequences for transcription factor binding sites, you retrieve JASPAR matrices via REST API, convert PFMs to PWMs, and perform sequence scanning with forward and reverse strand awareness to detect potential TF binding sites.

PFM (Position Frequency Matrix) represents the raw nucleotide counts at each position, while PWM (Position Weight Matrix) converts these frequencies into log-odds scores to quantify binding affinity for sequence scanning.

Yes, you can assess regulatory variant effects by scanning sequences with JASPAR PWMs to interpret motif disruption or creation, supporting GWAS and fine-mapping contexts for variant interpretation.

Transcription factor binding site scanning works on both forward and reverse strands, applying strand awareness during sequence scanning to ensure comprehensive detection of potential TF binding sites across user-provided DNA sequences.

You retrieve JASPAR TF binding profiles by querying REST endpoints to fetch matrices, which can then be converted into PWMs and applied to motif enrichment workflows across different species.

JASPAR transcription factor binding matrices support motif enrichment workflows and regulatory genomics analyses across multiple species, allowing you to query and retrieve species-specific TF binding profiles via the REST API.