RNA secondary structure alignment

[newBioinfo]

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



Thanks!!!

[ppgardne]

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

[newBioinfo]

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

[ppgardne]

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.

[newBioinfo]

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!!!