jaspar-database

What it does

Provides access to JASPAR 2024 TF binding profiles via REST API and pyJASPAR to retrieve PFMs/PWMs by TF name, JASPAR ID, species, or structural class; allows scanning DNA for TFBS and browsing by taxon or TF family. Notes use for motif enrichment input, TFBS scanning, and regulatory sequence analysis, with guidance to use homer-motif-analysis for de novo motif discovery from ChIP-seq peaks and regulomedb-database for regulatory variant scoring.

How it works

• Queries the JASPAR REST API at https://jaspar.elixir.no/api/v1/ to search for TF matrices by name, species, collection, tax_id, tax_group, tf_class, or tf_family; returns a paginated list of results with fields like matrix_id, name, sites, type, and metadata.
• Retrieves full matrix records for a given matrix_id (e.g., MA0139.1) including the raw PFM under pfm and metadata such as collection, species, class_name, and family_name.
• Demonstrates conversion from PFM to PWM via a function that adds pseudocounts, computes frequencies, and computes log-odds against a background distribution.
• Scans DNA sequences by sliding the PWM across the sequence, computing scores at each position, and reporting hits that exceed a defined threshold relative to max/min scores.
• Supports browser-based retrieval by tax_id to list PROFILEs for a given organism, and by TF class or TF family to assemble targeted motif libraries.
• Includes examples for quick start, core API usage, and common workflows like building a human TF motif library and exporting to MEME format.

When to use it

• When you need the PWM or PFM for a specific TF by name (e.g., CTCF) to use as motif input for scanning tools.
• When you want all JASPAR profiles for a species (e.g., Homo sapiens) to build a motif library for enrichment analysis.
• When scanning a DNA promoter sequence for predicted TF binding sites using a known PWM.
• When finding TFs of a given structural class (e.g., bHLH) or family to build a TF family binding profile set.
• When you need metadata like number of binding sites, information content, or GC content for a matrix.

What it can touch

• Accesses network APIs at https://jaspar.elixir.no/api/v1 to fetch matrices and metadata.
• Uses Python libraries such as requests, pandas, numpy, and optionally pyJASPAR as values from prerequisites.
• Data touched include matrix_id, name, collection, species, sites, type, pfm, and other metadata described in the API responses.

Caveats

• License: CC-BY-4.0
• Requires internet connection; no API key required for the REST API.
• Rate limits are not officially published; users are advised to insert sleep intervals (e.g., between batch requests) to avoid throttling.
• The workflow advises that for de novo motif discovery from ChIP-seq peaks, use homer-motif-analysis instead of JASPAR, and for regulatory variant scoring use regulomedb-database.