Rna Secondary Structure Homolgy Search

Question

[Nicolas Rosewick]

Hi,

I've several sequences and I want to check if there is known secondary structure into these sequences. Is there a tool to check if there are structure homolgies with known transcripts (mRNA,tRNA,miRNA,...)

Thanks

N.

Answer 1

[Medhat]

I think this software may help PHMMTS it will Do local alignment to an unfolded sequence by folded structure.

Answer 2

[JC]

Try Sean Eddy's Infernal with RFAM models.