Shortcomings
The MEME algorithms has several drawbacks including:
- Allowance for gaps/substitutions/insertions not included.
- Ability to test significance often not included.
- Erased input data each time a new motif is discovered (the algorithm assumes the new motif is correct).
- Limitation to two component case.
- Time complexity is high.
- Very pessimistic about alignment (which might lead to missed signals).
Read more about this topic: Multiple EM For Motif Elicitation
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