In fact, the Vienna package offers many very good RNA tools.
• 0 views
•
link
written
by
Larry_Parnell
Stem-Loop Rna Structure Prediction And Visualisation
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.
• 7,122 views
•
link
updated
by
Michael Dondrup
•
written
by
Nicolas Rosewick
•
written
by
Nicolas Rosewick
1 answer
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
• 0 views
•
link
written
by
Michael Dondrup
I tried but it get me only a postscript with the secondary structure
• 0 views
•
link
written
by
Nicolas Rosewick
so? you want to get exactly that textual representation?
• 0 views
•
link
written
by
Michael Dondrup
yes. I don't know if it is possible with the vienna package. Or maybe convert the dot-bracket notation to this notation ?
• 0 views
•
link
written
by
Nicolas Rosewick
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.
• 0 views
•
link
written
by
Michael Dondrup
yes it's for very simple structures (hairpin-like ones). Good idea I'll try a little perl script
• 0 views
•
link
written
by
Nicolas Rosewick
oki, keep in mind to pad the shorter end with spaces if the number of terminal dots on either side is not equal.
• 0 views
•
link
written
by
Michael Dondrup
Log in to answer this question.
More posts like this
Do you want to predict the structure or are you looking for a method to visualize already predicted structures?