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I used FIMO to scan several of my promoter sequences for TF binding motifs. The output .tsv file gives me the motif name/sequence plus the start and stop location, how can I visualize these outputs to get a graph that shows each motif as differing length rectangles along each promoter sequence, along with a gradient that shows the p-value?

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Potential workaround: use MAST.

As far as I understand, 'under the hood', so to speak, FIMO and MAST work pretty much the same. The difference might be just that FIMO focuses on scoring motifs, while MAST is scoring sequences (https://groups.google.com/g/meme-suite/c/qMSj6AdFxoM)

Example of FIMO output: https://web.mit.edu/meme_v4.11.4/share/doc/examples/fimo_example_output_files/fimo.html

Example of MAST output: https://web.mit.edu/meme_v4.11.4/share/doc/examples/mast_example_output_files/mast.html

There might be small differences in the output of the tools, but then it's up to you to see whether this is relevant for your data.

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  • $\begingroup$ FIMO and MAST have entirely different purposes. FIMO identifies statistically significant matches to motifs in a collection of sequences. MAST identifies the sequences that have the best overall match to a collection of motifs. The output of MAST does include a cartoon showing the motif matches for a particular sequence, it only does this for the sequences that have the best overall match to ALL the motifs in the input. It won't necessarily show the best matches to individual motifs. The typical use case for MAST is identifying promoter sequences regulated by multiple transcription factors. $\endgroup$ Dec 23, 2023 at 20:56
  • $\begingroup$ (cont) While internally MAST does perform a step equivalent to FIMO the final MAST output is not equivalent to the FIMO output. $\endgroup$ Dec 23, 2023 at 21:16
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If the sequences you are scanning with FIMO are supported by the UCSC or Ensembl genome browsers you can upload the GFF file generated by FIMO as a custom track: UCSC Custom Track, ENSEMBL Custom Track. Note that for the Ensembl website the FIMO GFF file is in GFF3 format.

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