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

Question

[Angel]

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

Answer 1

[Michael]

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.

Answer 2

[Pierre Lindenbaum]

Did you try the RNAfold web server?

[Larry_Parnell]

This is the site to which I first submit sequences.

[Angel]

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

[Michael]

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.

Answer 3

[Southwan]

the Mfold tools