1. RNA SECONDARY STRUCTURE PREDICTION TOOLS
RNA consists of a long chain of nucleotide units. RNA is transcribed from
DNA by enzymes called RNA polymerases . RNA is central to protein
synthesis via a type of RNA called messenger RNA carries information from
DNA to structures called ribosomes.
CONTENT
INTRODUCTION
SYNTHESIS
TYPES OF RNA
RNA SECONDARY STRUCTURE
TOOLS
MFOLD
VIENNA RNA PACKAGE
•RNAFOLD
SFOLD

2. SYNTHESIS

3. TYPES OF RNA
1. Messenger RNAs (mRNAs): The genetic coding templates used by the
translation machinery to determine the order of amino acids in the process
of translation.
2. Transfer RNAs (tRNAs): They form covalent attachments to individual amino
acids and recognize the encoded sequences of the mRNAs
3. Ribosomal RNAs (rRNAs): They assembled, together with numerous ribosomal
proteins, to form the ribosome. The proteins of the ribosomes catalyze all of the
functions of polypeptide synthesis.

4. RNA secondary structures
RNA is made of 4 nucleotides
A, G, C, U
RNA molecule are single-stranded but they can interact with themselves to
form secondary structures
The most typical RNA secondary structure is the hairpin
Hairpins are usually mad of a stem and a loop as shown here

5. TOOLS
•It is possible to predict the secondary structure of an RNA sequence
•The accuracy is ~70%
•Predictions are easier and more accurate on small molecules (fewer
than 500 nucleotides)
•More accurate predictions can be made using multiple-sequence
alignments
•RNA secondary structure is often predicted from sequence by free
energy minimization.
TOOLS USED
•MFOLD
•Vienna (RNA) package
rna fold
•SFold

6. Single-Sequence Structure
Prediction for RNA
Mfold is an RNA and DNA folding package developed by Dr. Michael Zuker..
mfold package for RNA and DNA secondary structure prediction using nearest
neighbor thermodynamic rules
The server predicts the most stable secondary structure (with the lowest
potential energy)
Mfold can also return suboptimal structures (indicate good accuracy)
Detailed output, in the form of structure plots with or without reliability
information, single strand frequency plots and 'energy dot plots', are available for
the folding of single sequences.
PSEUDOKNOTS ARE NOT CONSIDERED BY MFOLD SERVER

7. Searching Databases
for tRNAs
Transfer RNAs are small RNA molecules
used to build proteins
 Each protein has 64 tRNAs
 One for each triplet of the genetic
code
 All tRNAs have the same structure

8. MFOLD HOME PAGE
Link: DNA
sec.str.prediction
INPUT: sequence of
Human phe-tRNA

9. Linear sequence of RNA
to be fold
Is maxi. energy diff. from
optimal structure
Maxi. No. of suboptimal
structure
Maxi no. of
unpaired
nucleotide
To be filled
for BATCH
JOB
Click it for structure
prediction

10. OUTPUT

11. HAIRPIN LOOP
INTERIOR
LOOP
MULTIBRANCH
LOOP
Optimal &Suboptimal str.
having:
dG(GIBBS FREE ENERGY)=-151.52
dG=-150.30
STEM
Suboptimal str.
dG=-150.30

12. Conclusion
We have described several new computer programs that have been designed to
enable the user to determine the reliability of predicted RNA secondary structures
relatively easily.
Colored dots are used to provide a simple overview of how well
determined an entire predicted structure and/or a predicted structural domain within a
larger folding is.
Although the same information can be obtained from dot plot
 Representations of optimal and suboptimal foldings that is created both by mfold and by
the Vienna package, the dot plot representation of RNA secondary structures is relatively
difficult to understand.