Tool For Recognize Conserved Structural Motifs Among Dna Sequences

Question

[Anima Mundi]

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.

Answer 1

[Hamish]

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.

[Anima Mundi]

Thank you, I will try to understand how DREME works; in case I will mark this as the accepted answer ;).