I have a set of RNA sequences that I would like to align in order to see more clearly where are the conserved regions.
What is the best way to do this ? should I use normal alignment softwares that do not incorporate secondary strcture
information or is it better to predict the secondary structure first and then use this information to align the sequences?
For identifying conserved stretches of primary sequence - then clustal or MUSCLE will do just fine in most cases. If you want it to be "aware" of the structure - then the R-COFFEE tool (part of TCOFFEE) works well - it has a "structure aware" part of it's MSA algorithm that is optimized to include RNA secondary structure predictions of your sequences. http://tcoffee.crg.cat You may also want to compare your results against LocARNA from Backofen's lab. http://www.bioinf.uni-freiburg.de/Software/