program to find common secondary structure of RNA from many sequences

[ishmael]

LocaRNA is a tool based on both sequences alignments and secondary structures.

http://www.bioinf.uni-freiburg.de/Software/LocARNA/

You may check it.

[zhlyang]

Thanks a lot. I will look at these sites.

I haven't actually tried this yet, but:

http://ural.wustl.edu/~xingxu/RNASampler/index.html#Download%20RNASampler

This might help too:
http://en.wikipedia.org/wiki/List_of...ction_software

[mgogol]

I haven't actually tried this yet, but:

http://ural.wustl.edu/~xingxu/RNASampler/index.html#Download%20RNASampler

This might help too:

http://en.wikipedia.org/wiki/List_of_RNA_structure_prediction_software

[zhlyang]

Does anybody happen to know whether there is a software to find potential consensus RNA secondary structure instead of sequence motif from many sequences?

Thanks a lot in advance.