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I'm currently learning how to use MEME-Suite (web tool) to find a specific known transcriptor binding site in the promoter region of 5 putative bacterial genes of interest, but the results obtained with just the five promtoer sequences have an E-value too high. What can I do to improve these results? Can I use as input some other reported sequences that have the motif I'm looking for without introducing any bias?

I used the option ZOOPS, with a background model of first order, and I limited the search to palindromes only, since I'm looking specifically for a 20 bp sequence with dyad symmetry. The input sequences are the promoter regions of each gene (200 pb upstream of the start codon).

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  • $\begingroup$ Hi Laura, can you indicate please which program from the MEME suite you used for your analysis? $\endgroup$ – thomas duge de bernonville May 29 at 13:34
  • $\begingroup$ I'm using MEME, but I'm not sure if it would be better to use other tools such as FIMO, since I'm looking for a known motif. $\endgroup$ – Laura Pineda May 29 at 16:28
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    $\begingroup$ Use FIMO as you say since you want to match a known motif to a set of query regions. Overrepresentation analysis with only 5 regions is not meaningful. $\endgroup$ – ATpoint May 29 at 21:52
  • $\begingroup$ As @ATpoint points out over-representation analysis with only 5 regions might not give you anything.. It's like asking what is so special about 5 ? You needa see more $\endgroup$ – StupidWolf May 30 at 11:43
  • $\begingroup$ I can suggest this for you. You can go in with a set of known motifs, and ask in your 5 regions whether there's anything that seems to occur more than expected. Of course this might be still shakey, but gives you something to start with. $\endgroup$ – StupidWolf May 30 at 11:45

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