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  • RNA secondary structure alignment

    Hi All,
    Is there any aligner that can align RNA based on secondary structure.



    Thanks!!!

  • #2
    There are a few. RNAforester is one. It's not the generally recommended approach.

    Comment


    • #3
      Thanks ppgarnde,
      Can Infernal in RDP databse can do this?

      Comment


      • #4
        Infernal is great. It is very accurate and fast. It will align sequences to structures based upon sequence information and structure. It is designed primarily for the homology search problem.

        I thought you were trying to align two or more structures to each other.

        Comment


        • #5
          Originally posted by ppgardne View Post
          Infernal is great. It is very accurate and fast. It will align sequences to structures based upon sequence information and structure. It is designed primarily for the homology search problem.

          I thought you were trying to align two or more structures to each other.
          Thanks ppgardne,
          I have reads from sequencing and I want to align these to ribosomal database based on secondary structure. I have aligned based on sequence and want to see if aligning based on secondary structure gives anything different.

          Thanks!!!

          Comment

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