evolutionarily conserved RNA secondary structures in multiple sequence alignment - how to (Jan/23/2010 )

Hi
I have an alignment of RNA sequences of the same region in mRNA from multiple organisms and I want to know is there any structure conservation. I have a experimental data of this region in human RNA so it will be grate to look on this region in other organisms

Can You help me to choose right way to do this?

best

blaszcz

May be this link could be useful for you http://www.openwetware.org/wiki/Wikiomics:RNA_secondary_structure_prediction#Comparative_structure_prediction

the right way to do it would be finding papers where people have published similar analyses to what you are aiming for.
ie considering things such as species codon usage, type of alignment to perform, and so on.

cheers.