Transcription factor binding scanner

Motif scanning does not prove a factor binds in your cell on a given day. It predicts where a position weight matrix (PWM) of known TFBS sequences from a database match your DNA reasonably well. It doesn’t mean they are functional, but they might be. This is still useful for scanning a promoter or 5′ region after you fetch it (e.g. from our Promoter Grabber). Comparing a wild-type sequence to a mutant or deletion before you order primers. Seeing whether a ChIP peak region is littered with AP-1, SP1, NF-κB-style motifs, and so on.

If you need the same gene in several species and care about conservation of sites, use the cross-species TF scanner instead. This page is for one DNA sequence and one motif library at a time.

The bundled library is in MEME format (tf_elements.meme.txt, loaded automatically). Each motif is a matrix of log-odds scores for A/C/G/T at each position. The scanner slides every motif along your sequence on the forward and reverse strands and scores each window.

Scoring is a log-likelihood ratio against a simple background. Each motif has its own min–max score range; the Min strength slider is a percentage of that range — higher means stricter, fewer hits.

The species filter limits which motifs are scanned, using JASPAR-style taxonomic links (human, mouse, rat, etc.). Motifs not annotated for that species are skipped. Hits below your cutoff are not listed. The table shows the strongest matches up to Top hits. Optional hide weaker overlapping hits keeps the strongest score when the same motif name stacks at nearly the same place. This helps keep the list of TFBS relatively uncluttered.

Sequences longer than about 35 kb are truncated so the page stays responsive in the browser.

1. Paste DNA (A/C/G/T only; > FASTA header lines are ignored).
2. Wait for the bundled MEME library to finish loading (or drop in your own .meme file).
3. Pick a species filter if you do not want the full library.
4. Set Min strength (75% is a reasonable starting point. Tighten if you get too much noise).
5. Click Scan.

After the results appear, use the binding map which displays hits on the sense strand above the line and hits on the antisense strand below the line. You can pan, zoom, hover over a site for the scores. Use the Hits table for a list of motif name, strand, coordinates, matched sequence, bits, and % of that motif’s range. You can move the strength slider again to filter without re-pasting DNA (the page rescans briefly). Tick the hide weaker overlapping hits tick box if one TF name paints a solid bar at one position.

Tips:

• Fetch the promoter first with Promoter Grabber if you only have a gene symbol.
• A noisy promoter with many TFBS results is normal at low thresholds. In this case, raise the slider or filter by species.
• Replace the library only if you know your MEME file is valid; the bundled set is what we use day to day.

Not a substitute for ChIP-seq, ATAC, or EMSA. Not a full genome browser. Not motif discovery (no de novo search). For publication-grade genome-wide scans, use established pipelines (FIMO, MEME Suite on a server, etc.). This tool is for fast, visual, local checks on a sequence you already care about.

• Cross-species TF scanner — orthologous promoters, conserved elements
• Promoter Grabber — fetch promoter DNA from NCBI
• Restriction digest analyser — plan cloning around your construct