Find the distance between motif in a group of fast sequences

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5.5 years ago

ra2967 ▴ 20

Hi all,

I have a list of one hundred sequences. I know using MEME that my sequences all have two conserved motifs for two transcriptions factors.

My question is: may I calculate the distance of one motif to the other for each one of the sequences? I think that these proteins are interacting and that the distance is being conserved through all the sequences (something aroung 36 base). The problem may be, in fact, solved by "text" tools, I imagine, but I have no idea where I should start.

Thanks!

Robert

ChIP-Seq Motif analysis • 1.2k views

ADD COMMENT • link 5.5 years ago by ra2967 ▴ 20

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if you know the positions (start and end) of motifs on any given sequence, then it is simple calculation ra2967

ADD REPLY • link 5.5 years ago by cpad0112 21k

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In each one of my fasta sequences, they are distributed in different position. I would like to know the distance in each sequences that separate the motif A and the motif B, what may be not the same.

As I told, it may be solved by "text analysis", but I do not know how.

ADD REPLY • link 5.5 years ago by ra2967 ▴ 20

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