jaspar-database

To scan DNA sequences for transcription factor binding sites, provide a DNA sequence and a TF name. The skill fetches profiles from the JASPAR REST API, converts PFMs to PWMs with pseudocounts, and performs strand-aware sequence scanning using a defined threshold to predict TF binding sites.

The JASPAR CORE collection provides curated, open-access transcription factor binding profiles used as references for regulatory genomics. It supplies the position frequency matrices needed to generate PWMs for predicting TF binding sites during promoter analysis and motif enrichment.

Yes, JASPAR motif scanning supports GWAS regulatory variant interpretation. By scanning DNA sequences with JASPAR PWMs, you can assess whether genetic variants alter predicted transcription factor binding sites, helping to identify potential regulatory mechanisms underlying GWAS signals.

You can search for transcription factor binding profiles by querying the JASPAR REST API with specific parameters for TF name, species, and class. This retrieves matching profile matrices from the CORE collection, which can then be converted to PWMs for downstream sequence scanning.

Yes, JASPAR motif scanning works for ChIP-seq and ATAC-seq motif enrichment analysis. You can use the generated PWMs to scan peak or accessible chromatin sequences to identify enriched transcription factor binding motifs, supporting functional interpretation of epigenomic data.

Yes, pseudocounts are required when converting position frequency matrices to PWMs for TFBS prediction. The skill applies pseudocounts during PWM generation to avoid zero-probability weights, ensuring strand-aware sequence scanning produces robust transcription factor binding site predictions.