Documentation PlantQTLdb Assistant Plant Motif Analysis with JASPAR and FIMO
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Getting Started with Assistant Gene Structure and Sequence Extraction Variant Annotation and Local QTL Evidence Functional Enrichment with g:Profiler Network Analysis with STRING Finding Sequencing Data with ENA Sequence Similarity Search with BLAST Plant Motif Analysis with JASPAR and FIMO DNA Analysis with Evo2 External Biological Evidence Sources Troubleshooting and Limitations

PlantQTLdb Assistant

Plant Motif Analysis with JASPAR and FIMO

find plant transcription-factor motifs and scan short DNA for predicted matches

Requires Research mode

Open PlantQTLdb Assistant

When to use it

Investigate possible regulatory sites in a promoter or another short DNA fragment. First identify the motif matrix, then scan a sequence with an explicit versioned matrix ID.

How to ask and what you receive

Find a plant motif

ask
Find JASPAR ABF1 plant motifs

what you receive

Plant CORE motif records with matrix IDs and names. Choose a specific version, such as MA0570.1, for scanning; a family name alone does not imply binding in your species.

Scan a demonstration sequence

ask
Use FIMO to scan the following DNA with JASPAR motif MA0570.1:
>motif_test
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAGGACACGTGGCACGACGGGAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA

what you receive

Predicted motif matches with matrix ID, start/end, strand, score and per-site P value, with JSON/CSV downloads. This artificial sequence contains a motif-like segment for testing; it is not an experimentally validated promoter.

Extract a promoter and scan it

ask
Extract the 2 kb promoter sequence of Arabidopsis AT1G01010, transcript_id=AT1G01010.1, and scan it with FIMO using MA0570.1

what you receive

Reference promoter extraction followed by scanning the extracted sequence. FIMO runs only if extraction succeeds; zero motif matches is possible. If transcript selection is needed, resolve that first.

Interpret matches

Coordinates are 1-based positions within the submitted sequence. They are not automatically reference-genome coordinates, even when the sequence came from a promoter extraction.

The scan uses a per-site P-value threshold of 1e-4 on both strands. P values are uncorrected per-site values, not a cross-motif FDR. Higher scores reflect a stronger motif match relative to background, not measured binding strength.

A sequence match is a hypothesis for follow-up. Chromatin accessibility, tissue context and experimental evidence are needed before claiming regulation.

Resource and species boundaries

  • At most 10 kb DNA and 10 plant CORE matrices per scan; at most 500 matches are returned, with truncation marked.
  • One bounded worker runs at a time. A busy request returns a retry message; there is no background queue to check later.
  • Sorghum/tomato promoter extraction is disabled while reference compatibility is unresolved. You can still supply DNA directly for a standalone motif scan.