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  • Align sequence on secondary strcuture

    Hi guys,

    Anyone knows if a tool to align sequence (RNA, DNA) on a secondary structure exists ? It's only for visualization of the alignment on a known structure.

    Thanks,

    N.

  • #2
    For secondary structure based alignments look at http://expasy.org/tools/#secondary.
    Hope that helps. Else if you want to do this for tertiary u can use modeller, for instance.

    best,


    Phil

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    • #3
      Thanks, but it's ok for the structure (I have it). What I want to do is align sequencing reads on this structure and see where the reads aligned on it.

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      • #4
        nobody knows ? I think such a tool will be useful

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        • #5
          In the case of RNA you could probably use Infernal and an Rfam model of your choice to align it against your RNA in question.


          Andreas

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