Noida Institute of Engineering and Technology, Greater

Noida

Subject Name: Bioinformatics II

Subject Code: KBT-603

Course Details: B. Tech Biotechnology

3rd Year/ Semester –VI

Unit-II

Name of Faculty:
Dr. Harmanpreet Meehnian
Department of Biotechnology
Dr. Harmanpreet Meehnian KBT-603 BI-II Unit-II 1
05/15/2023
 Introduction of Faculty

Dr. Harmanpreet Meehnian (M. Tech - Ph.D)

Assistant Professor
(Department of Biotechnology, NIET Greater Noida)

Qualification:
Ph.D (Biotechnology)
(National Institute of Technology, Jalandhar)
B.Tech – M.Tech (Biotechnology)
(Lovely Professional University, Punjab)

Specialization: Enzyme and Microbial Technology

Teaching Experience : 2 years (National Institute of Technology, Jalandhar)
Industrial Experience: 1 year (Pharmacovigilance Scientist at Parexel International)
Email id: harmanpreet.meehnian@niet.co.in
er.harman2011@gmail.com
Research gate id: https://www.researchgate.net/profile/Harmanpreet-Meehnian

Dr. Harmanpreet Meehnian KBT-603 BI-II Unit-II 2

05/15/2023
 Evaluation Scheme

05/15/2023 Dr. Harmanpreet Meehnian KBT-603 BI-II Unit-II 3

 Subject Syllabus

05/15/2023 Dr. Harmanpreet Meehnian KBT-603 BI-II Unit-II 4

 Branch wise Applications

Bioinformatics finds applications in various sectors. Here is a

list of application of bioinformatics in various fields including:
1. Biotechnology
2. Alternative Energy Sources
3. Drug Discovery
4. Preventive Medicine
5. Biofuels
6. Plant Modelling
7. Gene Therapy
8. Waste Clean-up
9. Climate Change
10. Stem Cell Therapy
11. Microbial Genome
12. Crop Improvement

05/15/2023 Dr. Harmanpreet Meehnian KBT-603 BI-II Unit-II 5

 Course Objectives

· To provide knowledge to analyze various computational methods

involved in protein modeling, RNA structure prediction and drug
designing

· To teach various concepts of machine learning, Artificial Neural

Networks, document clustering

05/15/2023 Dr. Harmanpreet Meehnian KBT-603 BI-II Unit-II 6

 Course Outcomes

Course outcome: After completion of this course students will be able to

Understand the various tools and techniques related to in silico modeling of

CO 1 K1,K2
biomolecules

CO 2 Analyze problems related to collection and analysis of biological data K2,K3

CO 3 Develop steady and time dependent solutions along with their limitations K3,K4

CO 4 Understand the basic concept of modeling of biomolecules K4

CO 4 Understands the methods of drug designing, protein docking K5

05/15/2023 Dr. Harmanpreet Meehnian KBT-603 BI-II Unit-II 7

 Programs Outcomes (POs)

1. Engineering knowledge
2. Problem analysis
3. Design/development of solutions
4. Conduct investigations of complex problems
5. Modern tool usage
6. The engineer and society
7. Environment and sustainability
8. Ethics
9. Individual and team work
10. Communication
11. Project management and finance
12. Life-long learning

05/15/2023 Dr. Harmanpreet Meehnian KBT-603 BI-II Unit-II 8

 COs and POs Mapping

PO1 PO2 PO3 PO4 PO5 PO6 PO7 PO8 PO9 PO10 PO11 PO12

CO1 2 2 1 2 2 1 1 - - 1 - 1

CO2 2 2 2 2 3 1 - - - - - 1

CO3 2 2 2 2 2 - - - - - - 1

CO4 1 2 2 2 3 1 - - - - - 1

CO5 1 2 2 2 3 1 - - - - - 1

05/15/2023 Dr. Harmanpreet Meehnian KBT-603 BI-II Unit-II 9

 Program Specific Outcomes (PSOs)

PSO 1: To apply knowledge of basic sciences and biotechnological techniques.

PSO 2: To design, optimize, analyze and scale up bioprocess to develop useful

products with societal consideration.

PSO 3: To generate, analyze and interpret biological data using In silico and other
relevant approaches.

05/15/2023 Dr. Harmanpreet Meehnian KBT-603 BI-II Unit-II 10

 COs and PSOs Mapping

PSO1 PSO2 PSO3

CO1 1 - 1

CO2 1 - 2

CO3 1 - 3

CO4 1 - 3

CO5 1 - 2

05/15/2023 Dr. Harmanpreet Meehnian KBT-603 BI-II Unit-II 11

 Program Educational Objectives (PEOs)

PEO 1: Student will acquire knowledge skills in the frontier areas of biotechnology
and will be able to solve societal problem individually and in the team.

PEO 2: Students will be able to think creatively and ethically about the use of
biotechnology to address local and global problems

PEO 3: Students will be able to implement the engineering principles to biological

systems for development of industrial applications, as well as entrepreneurship skills
to start biotech industries.

05/15/2023 Dr. Harmanpreet Meehnian KBT-603 BI-II Unit-II 12

 Result analysis

Not Applicable

05/15/2023 Dr. Harmanpreet Meehnian KBT-603 BI-II Unit-II 13

 End Semester Question Paper Templates

05/15/2023 Dr. Harmanpreet Meehnian KBT-603 BI-II Unit-II 14

 Prerequisite and Recap

• A prerequisite for this course is the knowledge of introductory

Bioinformatics, Biochemistry, Genetics, Molecular Biology & Computer
Science.

05/15/2023 Dr. Harmanpreet Meehnian KBT-603 BI-II Unit-II 15

 Introduction about the subject with video

https://www.youtube.com/watch?v=zvyv_snBih8

https://www.youtube.com/watch?v=w-uk-_TOgR0

https://www.youtube.com/watch?v=lnRkKopf6GU

05/15/2023 Dr. Harmanpreet Meehnian KBT-603 BI-II Unit-II 16

 Topic Objective/ Topic Outcome

In this unit students learned about

• Basics of RNA Structure prediction and its limitations

• Features of RNA Secondary Structure

• RNA structure prediction methods: Based on self complementary regions in

RNA sequence

• Minimum free energy methods, Suboptimal structure prediction by MFOLD

• Prediction based on finding most probable structure and Sequence co-variance

method

• Application of RNA structure modeling

05/15/2023 Dr. Harmanpreet Meehnian KBT-603 BI-II Unit-II 17

 Unit Content (CO2)

• Basics of RNA Structure prediction and its limitations

• Features of RNA Secondary Structure

• RNA structure prediction methods: Based on self complementary regions in

RNA sequence

• Minimum free energy methods, Suboptimal structure prediction by MFOLD

• Prediction based on finding most probable structure and Sequence co-variance

method

• Application of RNA structure modeling

05/15/2023 Dr. Harmanpreet Meehnian KBT-603 BI-II Unit-II 18

 Unit Objective (CO2)

• Understanding the basics of RNA Structure prediction and its limitations

• Understand the features of RNA Secondary Structure

• RNA structure prediction methods : Based on self complementary regions in RNA

sequence

• Minimum free energy methods, Suboptimal structure prediction by MFOLD

• Prediction based on finding most probable structure and Sequence co-variance

method

• Application of RNA structure modeling

05/15/2023 Dr. Harmanpreet Meehnian KBT-603 BI-II Unit-II 19

 RNA Structure Prediction (CO2)

RNA Basics
• RNA bases A,C,G,U
• Canonical Base Pairs
– A-U
– G-C
– G-U
“wobble” pairing
– Bases can only pair with
one other base.

05/15/2023 Dr. Harmanpreet Meehnian KBT-603 BI-II Unit-II 20

 RNA Structure Prediction (CO2)

• Transfer RNA (tRNA)

• Messenger RNA (mRNA)
• Ribosomal RNA (rRNA)
• Small interfering RNA (siRNA)
• Micro RNA (miRNA)
• Small nucleolar RNA (snoRNA)

05/15/2023 Dr. Harmanpreet Meehnian KBT-603 BI-II Unit-II 21

 RNA Structure Prediction (CO2)

RNA Secondary Structure

Pseudoknot

Stem

Interior Loop

Single-Stranded

Bulge Loop
Junction (Multiloop)
Hairpin loop

05/15/2023 Dr. Harmanpreet Meehnian KBT-603 BI-II Unit-II 22

 RNA Structure Prediction (CO2)

RNA Secondary Structure

05/15/2023 Dr. Harmanpreet Meehnian KBT-603 BI-II Unit-II 23

 RNA Structure Prediction (CO2)

RNA Secondary Structure

05/15/2023 Dr. Harmanpreet Meehnian KBT-603 BI-II Unit-II 24

 RNA Structure Prediction (CO2)

RNA Secondary Structure

05/15/2023 Dr. Harmanpreet Meehnian KBT-603 BI-II Unit-II 25

 RNA Structure Prediction (CO2)

Pseudoknots

• Pseudoknots: a nucleic acid secondary structure containing at

least two stem-loop structures which half of one stem is
intercalated between the two halves of another stem.

05/15/2023 Dr. Harmanpreet Meehnian KBT-603 BI-II Unit-II 26

 RNA Structure Prediction Method (CO2)

Sequence Alignment as a method to determine structure

• Bases pair in order to form backbones and determine the secondary

structure
• Aligning bases based on their ability to pair with each other gives an
algorithmic approach to determining the optimal structure

05/15/2023 Dr. Harmanpreet Meehnian KBT-603 BI-II Unit-II 27

 RNA Structure Prediction Method (CO2)

Base Pair Maximization – Dynamic

Programming Algorithm

Simple Example:
Maximizing Base Pairing

S(i,j) is the folding of the subsequence of the RNA strand

from index i to index j which results in the highest number of
base pairs
05/15/2023 Dr. Harmanpreet Meehnian KBT-603 BI-II Unit-II 28
Images – Sean Eddy
 RNA Structure Prediction Method (CO2)

Simple Example:
Maximizing Base Pairing

Base pair at i and j

05/15/2023 Dr. Harmanpreet Meehnian KBT-603 BI-II Unit-II 29

 RNA Structure Prediction Method (CO2)

Simple Example:
Maximizing Base Pairing

Unmatched at i

05/15/2023 Dr. Harmanpreet Meehnian KBT-603 BI-II Unit-II 30

 RNA Structure Prediction Method (CO2)

Simple Example:
Maximizing Base Pairing

Umatched at j

05/15/2023 Dr. Harmanpreet Meehnian KBT-603 BI-II Unit-II 31

 RNA Structure Prediction Method (CO2)

Simple Example:
Maximizing Base Pairing

Bifurcation

05/15/2023 Dr. Harmanpreet Meehnian KBT-603 BI-II Unit-II 32

 RNA Structure Prediction Method (CO2)

Base Pair Maximization – Dynamic Programming Algorithm

 Alignment Method
 Align RNA strand to itself
 Score increases for feasible
base pairs
 Each score independent of
overall structure
 Bifurcation adds extra
dimension

05/15/2023 Dr. Harmanpreet Meehnian KBT-603 BI-II Unit-II 33

 RNA Structure Prediction Method (CO2)

 Alignment Method
 Align RNA strand to itself
 Score increases for feasible
base pairs
 Each score independent of
overall structure
 Bifurcation adds extra
dimension

Initialize first two diagonal

arrays to 0
05/15/2023 Dr. Harmanpreet Meehnian KBT-603 BI-II Unit-II 34
 RNA Structure Prediction Method (CO2)

 Alignment Method
 Align RNA strand to itself
 Score increases for feasible
base pairs
 Each score independent of
overall structure
 Bifurcation adds extra
dimension

Fill in squares
sweeping diagonally
05/15/2023 Dr. Harmanpreet Meehnian KBT-603 BI-II Unit-II 35
 RNA Structure Prediction Method (CO2)

 Alignment Method
 Align RNA strand to itself
 Score increases for feasible
base pairs
 Each score independent of
overall structure
 Bifurcation adds extra
dimension

Bases cannot pair, similar

to unmatched alignment

05/15/2023 Dr. Harmanpreet Meehnian KBT-603 BI-II Unit-II 36

 RNA Structure Prediction Method (CO2)

 Alignment Method
 Align RNA strand to itself
 Score increases for feasible
base pairs
 Each score independent of
overall structure
 Bifurcation adds extra
dimension

Bases can pair, similar

to matched alignment

05/15/2023 Dr. Harmanpreet Meehnian KBT-603 BI-II Unit-II 37

 RNA Structure Prediction Method (CO2)

 Alignment Method
 Align RNA strand to itself
 Score increases for feasible
base pairs
 Each score independent of
overall structure
 Bifurcation adds extra
dimension

Dynamic Programming –
possible paths
S(i + 1, j – 1) +1
05/15/2023 Dr. Harmanpreet Meehnian KBT-603 BI-II Unit-II 38
 RNA Structure Prediction Method (CO2)

 Alignment Method S(i, j – 1)

 Align RNA strand to itself
 Score increases for feasible
base pairs
 Each score independent of
overall structure
 Bifurcation adds extra
dimension

Dynamic Programming –
possible paths

05/15/2023 Dr. Harmanpreet Meehnian KBT-603 BI-II Unit-II 39

 RNA Structure Prediction Method (CO2)

 Alignment Method
 Align RNA strand to itself
S(i + 1, j)
 Score increases for feasible
base pairs
 Each score independent of
overall structure
 Bifurcation adds extra
dimension

Dynamic Programming –
possible paths

05/15/2023 Dr. Harmanpreet Meehnian KBT-603 BI-II Unit-II 40

 RNA Structure Prediction Method (CO2)

 Alignment Method
 Align RNA strand to itself
 Score increases for feasible
base pairs
 Each score independent of
overall structure
 Bifurcation adds extra
dimension

k = 0 : Bifurcation
Bifurcation – add values max in this case

for all k S(i,k) + S(k + 1, j)

05/15/2023 Dr. Harmanpreet Meehnian KBT-603 BI-II Unit-II 41

 RNA Structure Prediction Method (CO2)

 Alignment Method
 Align RNA strand to itself
 Score increases for feasible
base pairs
 Each score independent of
overall structure
 Bifurcation adds extra
dimension

Reminder:
Bifurcation – add values For all k

for all k S(i,k) + S(k + 1, j)

05/15/2023 Dr. Harmanpreet Meehnian KBT-603 BI-II Unit-II 42

 RNA Structure Prediction Method (CO2)

 Alignment Method
 Align RNA strand to itself
 Score increases for feasible
base pairs
 Each score independent of
overall structure
 Bifurcation adds extra
dimension

Reminder:
Bifurcation – add values For all k

for all k S(i,k) + S(k + 1, j)

05/15/2023 Dr. Harmanpreet Meehnian KBT-603 BI-II Unit-II 43

 RNA Structure Prediction drawbacks (CO2)

Base Pair Maximization - Drawbacks

• Base pair maximization will not necessarily lead to the most

stable structure

– May create structure with many interior loops or hairpins which are

energetically unfavorable

• Comparable to aligning sequences with scattered matches –

not biologically reasonable

05/15/2023 Dr. Harmanpreet Meehnian KBT-603 BI-II Unit-II 44

 RNA Structure Prediction drawbacks (CO2)

Base Pair Maximization - Drawbacks

05/15/2023 Dr. Harmanpreet Meehnian KBT-603 BI-II Unit-II 45

 RNA Structure Prediction (CO2)

Energy Minimization

• Thermodynamic Stability

– Estimated using experimental techniques

– Theory : Most Stable is the Most likely

• No Pseudknots due to algorithm limitations

• Uses Dynamic Programming alignment technique

• Attempts to maximize the score taking into account

thermodynamics

• MFOLD and ViennaRNA

05/15/2023 Dr. Harmanpreet Meehnian KBT-603 BI-II Unit-II 46
 Suboptimal structure prediction by MFOLD (CO2)

• This method uses the energy rules developed by Turner and colleagues to determine
optimal and suboptimal secondary structures for an RNA molecule and the energy
rules compiled and developed by Santa Lucia and colleagues to determine optimal
and suboptimal secondary structures for a single-stranded DNA molecule.
• Using energy minimization criteria, any predicted "optimal" secondary structure for
an RNA or DNA molecule depends on the model of folding and the specific folding
energies used to calculate that structure.

• MFold calculates energy matrices that determine all optimal and suboptimal
secondary structures for an RNA or DNA molecule. The program writes these energy
matrices to an output file. A companion program, PlotFold, reads this output file and
displays a representative set of optimal and suboptimal secondary structures for the
molecule within any increment of the computed minimum free energy you choose.
You can choose any of several different graphic representations for displaying the
secondary structures in PlotFold.

05/15/2023 Dr. Harmanpreet Meehnian KBT-603 BI-II Unit-II 47

 Suboptimal structure prediction by MFOLD (CO2)

05/15/2023 Dr. Harmanpreet Meehnian KBT-603 BI-II Unit-II 48

 Minimum free energy methods (CO2)
Energy Minimization Results

• Linear RNA strand folded back on itself to create secondary

structure
• Circularized representation uses this requirement
– Arcs represent base pairing

05/15/2023 Dr. Harmanpreet Meehnian KBT-603 BI-II Unit-II 49

 Minimum free energy methods (CO2)

Energy Minimization Drawbacks

Compute only one optimal structure

Usual drawbacks of purely mathematical approaches
Similar difficulties in other algorithms
Protein structure
Exon finding

05/15/2023 Dr. Harmanpreet Meehnian KBT-603 BI-II Unit-II 50

 Alternative Algorithms (CO2)

Alternative Algorithms - Covariation

• Incorporates Similarity-based method
– Evolution maintains sequences that are important
– Change in sequence coincides to maintain structure through base pairs
(Covariance)
• Cross-species structure conservation example – tRNA
• Manual and automated approaches have been used to identify covarying
base pairs
• Models for structure based on results
– Ordered Tree Model
– Stochastic Context Free Grammar

05/15/2023 Dr. Harmanpreet Meehnian KBT-603 BI-II Unit-II 51

 Alternative Algorithms (CO2)

05/15/2023 Dr. Harmanpreet Meehnian KBT-603 BI-II Unit-II 52

 Alternative Algorithms (CO2)

05/15/2023 Dr. Harmanpreet Meehnian KBT-603 BI-II Unit-II 53

 Alternative Algorithms (CO2)

05/15/2023 Dr. Harmanpreet Meehnian KBT-603 BI-II Unit-II 54

 Alternative Algorithms (CO2)

05/15/2023 Dr. Harmanpreet Meehnian KBT-603 BI-II Unit-II 55

 Alternative Algorithms (CO2)

05/15/2023 Dr. Harmanpreet Meehnian KBT-603 BI-II Unit-II 56

 Alternative Algorithms (CO2)

05/15/2023 Dr. Harmanpreet Meehnian KBT-603 BI-II Unit-II 57

 Alternative Algorithms (CO2)

05/15/2023 Dr. Harmanpreet Meehnian KBT-603 BI-II Unit-II 58

 Alternative Algorithms (CO2)

Expect areas of base

pairing in tRNA to be
covarying between
various species

05/15/2023 Dr. Harmanpreet Meehnian KBT-603 BI-II Unit-II 59

 Alternative Algorithms (CO2)

Base pairing creates

same stable tRNA
structure in organisms

Dr. Harmanpreet Meehnian KBT-603

05/15/2023 60
BI-II Unit-II
 Alternative Algorithms (CO2)

Mutation
Expect
Base areas
in one
pairing of base
base
creates
same
yields
pairingstable
pairing
in tRNA
tRNAto be
structure
impossible
covaryinginbetween
and
organisms
breaks
various
down structure
species

05/15/2023 Dr. Harmanpreet Meehnian KBT-603 BI-II Unit-II 61

 Alternative Algorithms (CO2)

Covariation
Mutation
Expect
Base areas
in ensures
pairing one
of base
base
creates
same
yields
ability
pairingstable
pairing
to
inbase
tRNA
tRNA
pair
to be
is
structure
impossible
maintained
covaryinginbetween
and
and
organisms
breaks
RNA
structure
various
down structure
species
is conserved

05/15/2023 Dr. Harmanpreet Meehnian KBT-603 BI-II Unit-II 62

 Alternative Algorithms (CO2)

Binary Tree Representation of RNA Secondary Structure

• Representation of RNA structure using
Binary tree
• Nodes represent
– Base pair if two bases are shown
– Loop if base and “gap” (dash) are
shown
• Traverse root to leaves, from left to right
• Pseudoknots still not represented
• Tree does not permit varying sequences
– Mismatches
– Insertions & Deletions

05/15/2023 Dr. Harmanpreet Meehnian KBT-603 BI-II Unit-II 63

 Covariance Model (CO2)

Covariance Model

• HMM which permits flexible alignment to an RNA structure –

– emission and transition probabilities
• Model trees based on finite number of states
– Match states – sequence conforms to the model:
• MATP – State in which bases are paired in the model and
sequence
• MATL & MATR – State in which either right or left bulges in
the sequence and the model
– Deletion – State in which there is deletion in the sequence when
compared to the model
– Insertion – State in which there is an insertion relative to model
• Transitions have probabilities
– Varying probability – Enter insertion, remain in current state, etc
– Bifurcation – no probability, describes path

05/15/2023 Dr. Harmanpreet Meehnian KBT-603 BI-II Unit-II 64

 Covariance Model (CO2)
Alignment to CM Algorithm

• For each calculation take into account

the
• Transition (T) to next state
• Emission probability (P) in the state as
determined by training data

05/15/2023 Dr. Harmanpreet Meehnian KBT-603 BI-II Unit-II 65

 Model construction (CO2)

Model Training

05/15/2023 Dr. Harmanpreet Meehnian KBT-603 BI-II Unit-II 66

 RNA Structure Prediction (CO2)
Mutual information for RNA Secondary Structure Prediction

05/15/2023 Dr. Harmanpreet Meehnian KBT-603 BI-II Unit-II 67

 Topic Links (CO2)

1. https://www.youtube.com/watch?v=kUN6rJ21Hno

2. https://www.youtube.com/watch?v=h60raqnvm0s

3. https://www.youtube.com/watch?v=v1UbIUZ8k9o

4. https://www.youtube.com/watch?v=ifkrWY5PoBs

5. https://www.youtube.com/watch?v=CU7A84aAvpw

05/15/2023 Dr. Harmanpreet Meehnian KBT-603 BI-II Unit-II 68

 MCQ s (CO2)

1. At present, there are essentially two types of method of RNA structure prediction. One is
the minimum free energy approach and the Second one is a comparative approach.
a) True
b) False
2. Ab initio approach makes structural predictions based on ______
a) a single RNA sequence
b) comparing RNA sequences
c) evolutionary basis
d) pure phylogenetics
3. In ab initio approach, generally, when a base pairing is formed, the energy of the molecule
is _________ because of attractive interactions between the two strands.
a) lowered
b) increased
c) multiplied
d) kept stable

05/15/2023 Dr. Harmanpreet Meehnian KBT-603 BI-II Unit-II 69

 MCQ s (CO2)

4. In ab initio methods, free energy can be calculated based on parameters empirically

derived for small molecules.
a) True
b) False
5. The energy necessary to form individual base pairs is not quite affected by adjacent
base pairs.
a) True
b) False
6. The attractive interactions lead to _________ energy.
a) increased
b) higher
c) lower
d) no change in

05/15/2023 Dr. Harmanpreet Meehnian KBT-603 BI-II Unit-II 70

 MCQ s (CO2)

8. Which is not a DNA sequencing method?

a. Sanger Method
b.Maxam-Gilbert method
c. NGS method
d.LC-MS
9. Which one is not a visualization tool?
e. Pymol
f. Rasmol
g.SwissPDB Viewer
h.Pride
10.VMD is used for….?
a. Sequencing
b.Database searching
c. Visualization
d.Storage

05/15/2023 Dr. Harmanpreet Meehnian KBT-603 BI-II Unit-II 71

 Old Question Papers (CO2)

05/15/2023 Dr. Harmanpreet Meehnian KBT-603 BI-II Unit-II 72

 Expected Questions for Exam (CO2)

1. Write down the min. free energy methods.

2. Discuss in detail RNA secondary str. Prediction methods.
3. Discuss the different forms of RNA.
4. Write a short note on partition function.
5. Discuss the different methods RNA secondary structure prediction.
6. What is the role of Dot Matrices & Dynamic programming in RNA structure prediction?
7. List out the different tools used for RNA secondary structure prediction and discuss in
brief.
8. What is base pair maximization? What are its drawback?
9. Describe in detail energy minimization?
10. Describe co-variance model for RNA structure prediction?
11. Draw a detailed diagram of a RNA molecule?
12. How RNA is different from DNA?

05/15/2023 Dr. Harmanpreet Meehnian KBT-603 BI-II Unit-II 73

 Recap of Unit (CO2)

RNA Basics
• RNA bases A,C,G,U
• Canonical Base Pairs
– A-U
– G-C
– G-U
“wobble” pairing
– Bases can only pair with
one other base.

05/15/2023 Dr. Harmanpreet Meehnian KBT-603 BI-II Unit-II 74

 Recap of Unit (CO2)

Pseudoknots
• Pseudoknots: a nucleic acid secondary structure containing at
least two stem-loop structures which half of one stem is
intercalated between the two halves of another stem.

05/15/2023 Dr. Harmanpreet Meehnian KBT-603 BI-II Unit-II 75

 Recap of Unit (CO2)

Simple Example:
Maximizing Base Pairing

Base pair at i and j

05/15/2023 Dr. Harmanpreet Meehnian KBT-603 BI-II Unit-II 76

 Recap of Unit (CO2)

• Their method uses the energy rules developed by Turner and colleagues to
determine optimal and suboptimal secondary structures for an RNA molecule and
the energy rules compiled and developed by SantaLucia and colleagues to
determine optimal and suboptimal secondary structures for a single-stranded DNA
molecule.
• Using energy minimization criteria, any predicted "optimal" secondary structure for
an RNA or DNA molecule depends on the model of folding and the specific folding
energies used to calculate that structure.

• MFold calculates energy matrices that determine all optimal and suboptimal
secondary structures for an RNA or DNA molecule. The program writes these energy
matrices to an output file. A companion program, PlotFold, reads this output file and
displays a representative set of optimal and suboptimal secondary structures for the
molecule within any increment of the computed minimum free energy you choose.
You can choose any of several different graphic representations for displaying the
secondary structures in PlotFold.

05/15/2023 Dr. Harmanpreet Meehnian KBT-603 BI-II Unit-II 77

 Recap of Unit (CO2)

Binary Tree Representation of RNA Secondary Structure

• Representation of RNA structure using
Binary tree
• Nodes represent
– Base pair if two bases are shown
– Loop if base and “gap” (dash) are
shown
• Traverse root to leaves, from left to right
• Pseudoknots still not represented
• Tree does not permit varying sequences
– Mismatches
– Insertions & Deletions

05/15/2023 Dr. Harmanpreet Meehnian KBT-603 BI-II Unit-II 78

 Recap of Unit (CO2)
Alignment to CM Algorithm

• For each calculation take into account

the
• Transition (T) to next state
• Emission probability (P) in the state as
determined by training data

05/15/2023 Dr. Harmanpreet Meehnian KBT-603 BI-II Unit-II 79

 References

•Bioinformatics: Databases, Tools & Algorithm by Orpita Basu & Siminder Thukral
•Bioinformatics Principles & Application by Zhumur Ghosh & Bibekanand Mallik.
•Bioinformatics Sequence & Genome Analysis by David W. Mount
•Essential Bioinformatics by Jin Xiong
•Fundamental Concepts of Bioinfromatics by Dan E. Krane & Michael L. Raymer

05/15/2023 Dr. Harmanpreet Meehnian KBT-603 BI-II Unit-II 80

 Noida Institute of Engineering & Technology

Thank You

05/15/2023 Dr. Harmanpreet Meehnian KBT-603 BI-II Unit-II 81