JASPAR RESTful API

JASPAR RESTful API provides programmatic access to curated transcription factor binding profiles, including position frequency matrices (PFMs) and transcription factor flexible models (TFFMs), to support studies of gene regulation.

Key Features:

• Curated non-redundant profiles: Provides curated, non-redundant transcription factor (TF) binding profiles across JASPAR CORE collections.
• Profile representations: Stores profiles as position frequency matrices (PFMs) and transcription factor flexible models (TFFMs).
• Supported output formats: Returns data in JSON, JSONP, JASPAR, MEME, PFM, TRANSFAC, BED, and YAML formats.
• Retrieval endpoints: Exposes multiple REST endpoints to retrieve different types of TF binding profiles, including an endpoint that infers likely TF binding profile(s) from a DNA-binding domain protein sequence.
• Implementation: Implemented using the Django REST Framework in Python.
• Programmatic clients: Accessible programmatically via additional packages such as the R/Bioconductor interface and pyJASPAR for Python-based access.

Scientific Applications:

• Transcription factor research: Enables study of TF binding specificity and gene regulation across taxonomic groups including vertebrates, plants, urochordates, and insects.
• Genome browser visualization: Supports generation of TF-binding site predictions that can be visualized as native tracks in the UCSC Genome Browser for human and mouse genomes.
• TFBS enrichment analysis: Facilitates transcription factor binding site (TFBS) enrichment analysis within user-provided genomic regions.
• Database expansion and classification: Supports analyses using expanded CORE collections, including newly added profiles and familial clustering with revised structural classifications (including plant-specific classifications).

Methodology:

Implements a REST architecture via Django REST Framework; exposes endpoints for profile retrieval and for inferring TF binding profiles from DNA-binding domain protein sequences; provides profiles as PFMs and TFFMs and exports in JSON, JSONP, JASPAR, MEME, PFM, TRANSFAC, BED, and YAML; recent CORE updates incorporate familial clustering and revised structural classifications.