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  • #1

    How to Scan Degenerate DNA 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.

    Thanks.
    Last edited by HSV-1; 01-19-2016, 10:47 PM.
    Tags: degenerate, dna motif, software
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