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Old 01-19-2016, 06:52 PM   #1
Location: asia

Join Date: Jul 2012
Posts: 38
Red face How to Scan Degenerate DNA motifs (TF binding sites)

Hi all,
I am interested in the genome-wide DNA motifs for transcription factors.
I am wondering if there are softwares I can use to scan degenerate DNA motifs.
For example I want to search YTATAATRnnnWW in mouse genome in one shot. The problem is that Y stands for pyrimidine, R for purines and n for anyone of A,C,G,T and W for A or T. So I can't simply treat the sequences.

It would be great if someone has this kind of software.


Last edited by HSV-1; 01-19-2016 at 09:47 PM.
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degenerate, dna motif, software

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