Stockholm format to dot-brackets format?

Question

I need to convert all my sequences in a Stockholm format into this:

hg19_11_6_Ala          ----------------.GG--gggaguggugu....gguuacgaaugUGGCCUCUGC-----AA.............................................................GCAGACA.........................G..CCUGGGUUCAAUU...........................
#=GR hg19_11_6_Ala  PP .................22..45677788888....899999999996777899988.....56.............................................................8999999.........................9..*************...........................

Into something like this:

 hg19_11_6_Ala         ................((..(((((((((((...)))))))))))))))))))))))....((................................)))))))))......)))).....................

Obviously, being coherent with the stockholm format. Any hint?

Answer 1

If what you want is to find a consensus structure for a group of alignments in stockholm format then you might try with RNAalifold and for single sequence folding check RNAfold. Both have online servers and can also be run offline.

After you get the consensus structure update the stockholm file by adding a structure consensus line as: #=GC SS_cons followed by the dot bracket notation.

A nice RNA structure editor that will make your life easier is EMACS when complemented with RALEE. It allows you to view and manipulate RNA structures, predict structure folding and color the alignments based on basepairs relationships. It will be worth it to invest time into mastering RALEE.