Seqanswers Leaderboard Ad

Collapse

Announcement

Collapse
No announcement yet.
X
 
  • Filter
  • Time
  • Show
Clear All
new posts

  • protein dna binding sites

    Hello,

    I have around 200 protein's fasta file. How can I find these proteins binding site with DNA?

    For example:It comes from Wikipedia.

    The AP-1 binding site, also known as the AP-1 promoter site, is a DNA sequence to which AP-1 transcription factors are able to bind. The AP-1 binding site, in humans, has a nucleotide sequence of ATGAGTCAT.

    Thanks in advance!

    Best,

    Yue

  • #2
    Are these proteins DNA-binding proteins, or are you wanting to find which DNA-binding proteins bind to the gene region of these proteins?
    Providing nextRAD genotyping and PacBio sequencing services. http://snpsaurus.com

    Comment


    • #3
      Hello, SNPsaurus,

      Thank you so much for your replying.

      I want to know the DNA sequencing which can binding to the protein.

      Thank you in advance for your great help!

      Best,

      Yue

      Comment


      • #4
        Hi Yue,

        To my knowledge, there is not a certain way to find a DNA sequence that a specific protein binds (accept for an experimental approach, of course).

        If there are solved structures of the 200 proteins with a strand of DNA, it is not hard to see which of the nucleotides is in contact with the protein.

        However, if we stay only at sequence level, I am not sure there is a relevant prediction method, at least to my knowledge.

        From sequence perspective, there are prediction tools designed to try and determine if a protein is DNA binding only based on sequence (our lab also has one- DR. PIP). A new prediction method to identify couples of proteins and the DNA they bind is currently being developed in our lab.

        Good luck!
        Sapir
        Last edited by SapirP; 09-04-2019, 05:57 AM.

        Comment


        • #5
          Hello, SapirP,

          Thank you so much for your answer.

          Thank you for the clue you give to me.

          Thank you again!

          With Best,

          Yue

          Comment


          • #6
            Thank you so much for your replying.

            Comment

            Latest Articles

            Collapse

            • seqadmin
              Strategies for Sequencing Challenging Samples
              by seqadmin


              Despite advancements in sequencing platforms and related sample preparation technologies, certain sample types continue to present significant challenges that can compromise sequencing results. Pedro Echave, Senior Manager of the Global Business Segment at Revvity, explained that the success of a sequencing experiment ultimately depends on the amount and integrity of the nucleic acid template (RNA or DNA) obtained from a sample. “The better the quality of the nucleic acid isolated...
              03-22-2024, 06:39 AM
            • seqadmin
              Techniques and Challenges in Conservation Genomics
              by seqadmin



              The field of conservation genomics centers on applying genomics technologies in support of conservation efforts and the preservation of biodiversity. This article features interviews with two researchers who showcase their innovative work and highlight the current state and future of conservation genomics.

              Avian Conservation
              Matthew DeSaix, a recent doctoral graduate from Kristen Ruegg’s lab at The University of Colorado, shared that most of his research...
              03-08-2024, 10:41 AM

            ad_right_rmr

            Collapse

            News

            Collapse

            Topics Statistics Last Post
            Started by seqadmin, Yesterday, 06:37 PM
            0 responses
            7 views
            0 likes
            Last Post seqadmin  
            Started by seqadmin, Yesterday, 06:07 PM
            0 responses
            7 views
            0 likes
            Last Post seqadmin  
            Started by seqadmin, 03-22-2024, 10:03 AM
            0 responses
            49 views
            0 likes
            Last Post seqadmin  
            Started by seqadmin, 03-21-2024, 07:32 AM
            0 responses
            66 views
            0 likes
            Last Post seqadmin  
            Working...
            X