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discover-motifs

Find recurring DNA sequence patterns in candidate footprint regions, without starting from a known motif list. Provide candidate intervals and a reference genome, or use sequences you have already extracted into a FASTA file.

Example command

discover-motifs --candidates project/samples/sample/footprints/sample_candidate_footprints.bed --genome hg38.fa.gz \
  --flank 75 --method streme --known-motif-db jaspar2026_vertebrates --outdir project/de_novo/sample --execute

Primary inputs

  • --candidates — candidate-footprint BED intervals.
  • --genome — reference FASTA matching the candidate coordinates; required with --candidates.
  • --flank — bases included on each side of a candidate center.
  • --method — discovery method; the example uses STREME.
  • --known-motif-db — optional known-motif database for Tomtom matching.
  • --outdir — directory for candidate FASTA files and discovery results.
  • --execute — run discovery immediately using the managed MEME Suite runtime.

In the example, --flank 75 extracts up to 75 bases on each side of each candidate center. Without --execute, the command writes the FASTA and a command script for inspection. It does not run discovery or create result summaries.

Main outputs

{outdir} is the selected discovery directory:

Path Meaning
{outdir}/candidate_sequences.fa Reference sequences extracted around candidate footprint intervals.
{outdir}/run_motif_discovery.sh Commands for discovery, optional known-motif matching, and summary reports.
{outdir}/streme/streme.txt, meme/meme.txt, or dreme/dreme.txt Discovered motif models from the selected method when --execute is used.
{outdir}/tomtom/tomtom.tsv Optional similarity matches to the selected known-motif database.
{outdir}/motif_summary.tsv and motif_summary.html Motif tables written after successful execution.

Open motif_summary.html to review discovered motifs and any known-motif matches. These matches suggest motif identities; similar TFs can share the same motif. To regenerate a summary from existing results, use summarize-motifs. See the complete discover-motifs reference.

Choose your sequence input

Create candidate intervals with call-footprints --output-bed. If you already have a sequence FASTA, pass it with --fasta instead of --candidates and --genome. In that case the command uses your existing sequences directly.