cbgr/jaspar-inference-tool repository overview

⁠JASPAR Profile Inference Tool

Infers JASPAR transcription factor (TF) binding profiles for a query DNA-binding domain(s) (DBDs) or full protein sequence(s) by scanning for DBDs via HMMER, performing sequence similarity search via BLAST+, and applying Cis-BP similarity regression models.

Built for the JASPAR 2026 release. For prior releases see wassermanlab/JASPAR-profile-inference⁠.

The image bundles all dependencies (BLAST+, HMMER, Python libraries) and pre-built JASPAR 2026 data. No internet access required at runtime.

Source and Dockerfile: https://github.com/amathelier/JASPAR-inference-tool⁠

⁠Supported taxons

fungi · insects · nematodes · plants · urochordates · vertebrates

⁠Usage

⁠Docker / Podman

docker pull cbgr/jaspar-inference-tool:2026

docker run --rm \
  -v /path/to/input:/data:ro \
  -v /path/to/output:/out \
  cbgr/jaspar-inference-tool:2026 \
  /data/query.fa --output-file /out/results.tsv

⁠Convert once

apptainer pull docker://docker.io/cbgr/jaspar-inference-tool:2026

⁠Infer profiles (TSV output)

apptainer exec \
  -B /path/to/input:/data:ro \
  -B /path/to/output:/out \
  jaspar-inference-tool_2026.sif \
  infer_profile /data/query.fa --output-file /out/results.tsv

⁠Infer profile with TSV and HTML visualisation report

Pass --html-output to generate a self-contained HTML report alongside the TSV. For each input sequence, the report shows inferred JASPAR profiles with sequence logos (SVG) and TF metadata (name, class, family):

docker run --rm \
    -v "$PWD":/data \
    cbgr/jaspar-inference-tool:2026 \
    --latest /data/sequences.fa \
    --output-file /data/results.tsv \
    --html-output /data/report.html

The HTML file is fully self-contained (with inline SVG logos and no external dependencies) and can be opened directly in any browser.

⁠Infer by homology

apptainer exec \
  -B /path/to/input:/data:ro \
  jaspar-inference-tool_2026.sif \
  infer_homolog /data/query.fa /data/target.fa

⁠Key options (infer_profile)

⁠Output TSV columns

Query · TF Name · TF Matrix · E-value · Query Start-End · TF Start-End · DBD %ID

⁠Tags

⁠References

• JASPAR 2026: Baydar Övek, Rauluseviciute, et al. NAR 2026⁠
• Similarity regression: Lambert et al., Nature Genetics 2019⁠
• JASPAR 2020: Fornes et al., NAR 2020⁠