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  • check for binding sites of transcription factors

    Hi all,
    I would like to find putative binding sites of transcription factors for a batch of nucleotide sequences correspond to promoters regions (input file should be a fasta file). Is any suggestion for a tool /software that it could be make this job??
    P.S. The promoter regions are from Arabidopsis.
    Thanks in advance--

  • #2
    I've used RSAT (http://embnet.ccg.unam.mx/rsa-tools/) for identifying enriched TF sites in putative enhancer regions of 400 bp. The linked site warns about false positives when using promoter regions, so keep that in mind.
    Providing nextRAD genotyping and PacBio sequencing services. http://snpsaurus.com

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