Match sequence against miRNA binding motifs
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In simple terms, you have a 5-mer sequence and would like to see if it hits any motif ( of miRNA ). You could use MEME (motif scanning suite) by inputting your sequences. But ideally, a motif will have a weight matrix for each nucleotide, then the search results becomes more reliable.
I only have a single 5-mer though, not many sequences. So I don't think MEME makes sense here. I did try TomTom from the MEME suite though, which seems to do something close to what I am looking for.