Hello,
I would like you to suggest me a tool capable to recognize structural conserved motifs among a MSA of DNA sequences of interest, rather than simply recognize a consensus in the nucleotide sequence.
For example, for the sequences:
1 ATTA
2 GTTG
3 CGGC
The common structure should be XYYX (X, Y are different incognite nucleotides).
Instead, for the sequences:
1 ATTA
2 ACGA
3 AGAA
The common structure should be ANNA. Hope this is clear enough.
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Anima Mundi
Not sure if this is what you are looking for, but a tool that comes to mind for discovering motifs in a set of DNA sequences is DREME, part of the MEME suite.
Thank you, I will try to understand how DREME works; in case I will mark this as the accepted answer ;).
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