Question

When using different analytical tools such as meme or scansite to find motifs of certain fasta sequence, you would get different results. By this, you would find that some substrates do not have any motif.

Is this reasonable to conclude like this? Provide some persuasive and analytical reasons to support your idea.

Answer 1

Question

No, it is not reasonable to conclude like this. This is because each tool is based on specific assumption and if our input sequence do not get any motif sequence, it just mean that out input sequence do not matching with tool assumption.

For example, meme tool is based on 0th order Markov model that is based on the assumption that character frequency at each position in the sequence are independent of one another. But this assumption is not valid for all sequence , for example CpG island sequence. On the other hand, scansite tool search for the motif which are likely to be phosphorylated or bind to any signalling domain. But not every sequence meet these assumptions and therefore it is not correct to conclude that our substrate do not have any motif.