Stem-Loop Rna Structure Prediction And Visualisation

Question

[Nicolas Rosewick]

Hi,

How can I produce such stem-loop structure from a sequence (like mirbase website).

c       guug   uc               g      u  ug 
 gggguug    uua  uuugguuaucuagcu uaugag gg  u
 |||||||    |||  ||||||||||||||| |||||| ||  g
 ccccaau    aau  aagccaauagaucga auacuu cu  g
a       -aaa   ga               a      -  ga

Thanks,

N.

[Andreas]

Do you want to predict the structure or are you looking for a method to visualize already predicted structures?

Answer 1

[Michael]

RNAfold should be able to do this.

Just checked it with your sequence, RNAfold yields exactly the same base pairing as in your example (which might not be very surprising though)

> RNAfold

Input string (upper or lower case); @ to quit
....,....1....,....2....,....3....,....4....,....5....,....6....,....7....,....8
cgggguugguuguuaucuuugguuaucuagcuguaugagugguguggaguc-uucauaaagcuagauaaccgaaaguaaaaa-uaacccca
length = 91
CGGGGUUGGUUGUUAUCUUUGGUUAUCUAGCUGUAUGAGUGGUGUGGAGUC-UUCAUAAAGCUAGAUAACCGAAAGUAAAAA-UAACCCCA
.(((((((....(((..(((((((((((((((.((((((.((.......)).)))))).)))))))))))))))..)))....))))))).
 minimum free energy = -42.60 kcal/mol

[Michael]

so? you want to get exactly that textual representation?

[Michael]

Disadvantage of your notation is that it only works for very simple structures with a single terminal loop! The dot-bracket notation (and the post-script) is more powerful. If there is only one loop however, creating a (e.g. perl) script that converts to this notatios is almost trivial, I would like toleave that to you as an exercise, but maybe there is one script out there already.

[Larry_Parnell]

In fact, the Vienna package offers many very good RNA tools.

[Nicolas Rosewick]

I tried but it get me only a postscript with the secondary structure

[Nicolas Rosewick]

yes. I don't know if it is possible with the vienna package. Or maybe convert the dot-bracket notation to this notation ?

[Nicolas Rosewick]

yes it's for very simple structures (hairpin-like ones). Good idea I'll try a little perl script

[Michael]

oki, keep in mind to pad the shorter end with spaces if the number of terminal dots on either side is not equal.