Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • 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

          Latest Articles

          Collapse

          • seqadmin
            Current Approaches to Protein Sequencing
            by seqadmin


            Proteins are often described as the workhorses of the cell, and identifying their sequences is key to understanding their role in biological processes and disease. Currently, the most common technique used to determine protein sequences is mass spectrometry. While still a valuable tool, mass spectrometry faces several limitations and requires a highly experienced scientist familiar with the equipment to operate it. Additionally, other proteomic methods, like affinity assays, are constrained...
            04-04-2024, 04:25 PM
          • 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

          ad_right_rmr

          Collapse

          News

          Collapse

          Topics Statistics Last Post
          Started by seqadmin, 04-11-2024, 12:08 PM
          0 responses
          17 views
          0 likes
          Last Post seqadmin  
          Started by seqadmin, 04-10-2024, 10:19 PM
          0 responses
          21 views
          0 likes
          Last Post seqadmin  
          Started by seqadmin, 04-10-2024, 09:21 AM
          0 responses
          16 views
          0 likes
          Last Post seqadmin  
          Started by seqadmin, 04-04-2024, 09:00 AM
          0 responses
          46 views
          0 likes
          Last Post seqadmin  
          Working...
          X