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A Web Server Which Gives Various Possible Secondary Structures From A Given Rna Sequence?

Could anyone tell me about any web server or tool which uses various kinds of algorithms and gives all possible structures from a given RNA sequence.

Thanks in advance

secondary prediction rna
• 3,735 views • link
updated by Biostar Biostar • written by Angel • Angel

3 answers

There are several algorithms in the BiBiServ RNA Studio. Have a look at the tools listed there for example:

  • paRNAss Prediction of Alternate RNA Secondary Structures
  • RNAfold calculate secondary structures of RNAs
  • RapidShapes RapidShapes computes the shapes above a specified probability threshold T by generating a list of promising shapes and constructing specialized folding programs for each shape to compute its probability. This aims at a heuristic improvement of runtime, while still computing exact probability values.
• 148 views • link
written by Michael Dondrup Michael Dondrup

Did you try the RNAfold web server?

• 1 views • link
updated by Ram Ram • written by Pierre Lindenbaum Pierre Lindenbaum

This is the site to which I first submit sequences.

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written by Larry_Parnell Larry_Parnell

the RNAfold server gives the best structure from the sequence. But i need all the secondary structure possibilities from the sequence.

• 0 views • link
written by Angel • Angel

Angel, you are right, RNAfold(2) is possibly the overall best tool, but to get alternative structuresor try different approaches you should really try at least paRNAss and RapidShapes.

• 0 views • link
written by Michael Dondrup Michael Dondrup

the Mfold tools

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written by Southwan • Southwan

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