CRS 7213 BIOINFORMATICS AND COMPUTATIONAL BIOLOGY
Lecturer (1)
Dr. Patrick Okori
PhD Plant Breeding and Genetics (Swedish University of agricultural Science- Uppsala
Sweden),
MSc Crop Science Makerere University
BSc Agriculture (Upper second Class Makerere University)
Member of African Crop Science Society, Member of International Society of Plant
Pathology
Senior Lecturer.
Course Type:
Core (MSc. Crop Science)
1. COURSE STRUCTURE
The course is a 3 credit units (2 contact hours per week for 15 weeks of study- 3 CU i.e. 45 Contact Hours per
semester) and 30 hours of practicals for 15 weeks of study (15 weeks (45 hours) i.e. 30 LH, 30 PH). All lectures will
take place at the School of Agricultural Sciences. All tutorials sessions will take place in the appropriately either at the
molecular and tissue culture laboratories or at research centres such as the National Biotechnology Centre as
necessary.
COURSE DESCRIPTION
The course will expose student to bioinformatics and computational biology. Key aspects of the course include; over
view of the subject, a review of evolution theory; measurable elements in evolution i.e. protein and DNA, RNA
sequences, managing data using the internet (database mining, BLAST and FASTA searches and alignments),
models for studying evolutionary changes, (Jukes and Cantor, Kimura 2 parameter, Tajima and Nei’s methods).
Molecular phylogenetics (distance and character based approaches). Predicting genes, RNA, proteins and function.
Large scale genomics, methods population genetics, mapping procedure such QTL analysis. Introduction to
comparative and functional genomics:
2. COURSE OBJECTIVES
General objective / aim
The general aim of this course is to equip students with knowledge and skills in bioinformatics and computational
biology
Specific objectives
1. To expose students to new advances in bioinformatics and computational biology and biotechnology.
2. To equip graduate students with knowledge and skills for conducting research in molecular biology using
bioinformatics tools .
3. RECOMMENDED REFERENCES FOR READING
1. Baxevanis, A.D and Ouellette, B.F.F. eds. 2001. Bioinformatics: A practical guide to analysis of genes and
proteins 2nd edition. John Wiley and Sons UK.
2. Balding, D.J., Bishop, M. and Canning, C eds. 2003. Handbook of Statistical Genetics 2nd Edition. John
Wiley and Sons UK.
3. European Bioinformatics Institute: www.ebi.ac.uk ( various online learning resources). The National Center
for Biotechnology Information (NCBI) (www.ncbi.nml.nih.gov) will be used for biomedical and genomic
information on line resources.
4. COURSE CONTENT, METHODS OF INSTRUCTION, TOOLS AND EQUIPMENT REQUIRED
TOPIC
CONTENT
METHOD OF
INSTRUCTION /
Time allocated
1. Introduction
Interactive Lecture
 Introduction to bioinformatics
(2 hrs)
 What it is; Internet basics
 Molecular evolution: Review of nucleic acids;
amino acids; proteins and genes gene families
superfamilies, motifs etc
2. Recombinant DNA
and DNA sequencing
and mapping
 Methods: Primer Design, Restriction
endonuclease mapping and translation
 Type of maps: genetic and physical
 Review of principles mapping and mapping
programmes (Quantitative trait loci for genetic
maps).
Interactive and
regular lecture (3
hrs)
 Overview of public data bases: Sequence
searches and retrieval (GCG, SRS (Week 3)
Interactive and
regular lecture (4
hrs)
 Alignment programmes (FASTA, BLAST,
Evaluating matches) (Week 3)



Jukes and Cantor, Kimura 2 Parameter,
Other Models. (Week 5)
Divergence among sequences. (Week 5)
Estimating number of substitutions between
sequences using the above models and
Tajima and Nei models and others. (Week 6).
Practical: Computer exercise on multiple
sequence alignment. This will be done during
LCD Projector
and
Screen,
BB/Chalk
Course Books
Bioinformatics: A
practical guide to
analysis of genes
and proteins and
hand book of
Statistical
genetics
 Principles, global versus local alignments,
repetitive elements, retro-transposons, dot plots
and multiple sequence alignments (Week 4)
4. Models for studying
evolutionary changes in
nucleotides
LCD Projector
and
Screen,
BB/Chalk
Course Books
Bioinformatics: A
practical guide to
analysis of genes
and proteins and
hand book of
Statistical
genetics
 Practical: Computer exercise on primer design
and Restriction endonuclease mapping. This
will be Started in week 2 and completed during
week 3 (4hrs).
3 Managing data using
internet based
resources
TOOLS /
EQUIPMENT
NEEDED
LCD Projector
and
Screen,
BB/Chalk
Lecture (4 hrs)
LCD Projector
and
Screen,
BB/Chalk
Course Books
Bioinformatics: A
practical guide to
weeks 5-6. (8hrs)
5. Theory: Predicting
Genes, protein structure
and function
Gene prediction, functional signal recognition,
splice site prediction (Week 7)
analysis of genes
and proteins and
hand book of
Statistical
genetics
Lecture (4 hrs)
Gene identification methods (grail. genscan etc)
(Week 7)
Review of protein structure, function and motif
searching and secondary structure prediction
(Week 8)
Course Books
Bioinformatics: A
practical guide to
analysis of genes
and proteins and
hand book of
Statistical
genetics
Take home: Statistical considerations in biological
sequence comparisons
6. RNA structure,
prediction and
regulatory functions

 Tools for predicting RNA structure and
regulatory functions
 Expresses sequence tags (ESTs)
LCD Projector
and
Screen,
BB/Chalk
Lecture (2 hrs)
LCD Projector
and
Screen,
BB/Chalk
Course Books
Bioinformatics: A
practical guide to
analysis of genes
and proteins and
hand book of
Statistical
genetics
7. Large scale genomics
analysis
Micro-array analysis – consideration for data
management and handling
.
Lecture (3 hrs)
LCD Projector
and Screen,
BB/Chalk
Extra reading and
take home
Course Books
assignment
Bioinformatics: A
practical guide to
analysis of genes
and proteins and
hand book of
Statistical
genetics
8. Phylogenetics

Basic concepts in molecular
phylogenetics (Week 11)
Lecture (4 hrs)
LCD Projector
and
Screen,

BB/Chalk
Methods: character based versus
distance based methods (Week 11-12)
Practical: Computer exercise using a Neighbor
joining and maximum parsimony. This will be done
during weeks 11-12. (8hrs)

9. Population genetics:
analytical methods and
tools




Evolution of orthologues and paralogues
(Week 13)
Review of key concepts on population
structure and evolutionary forces (Week
14)
Analysis of molecular variation, exact
tests, gene diversity (Week 15)
Seminar: Group seminars given by students
on basis of journal article reviews
Final exam: set along with University exams
5. SUMMARY OF TIME NEEDED
Interactive lectures and seminars covering theory
Tutorials and seminars
15 hrs
16
6. OVERALL COURSE EVALUATION
Continuous Assessment Test
20%
 At least 2 tests ( first after lecture 10 and second after lecture 15)
 Marked out of 20 each
Continuous Assessment (Assignments, practicals)
 Take home assignment
 Practical reports cumulatively add up to 20 marks
20%
Final examination
60%
END
Course Books
Bioinformatics: A
practical guide to
analysis of genes
and proteins and
hand book of
Statistical
genetics
Lecture (4 hrs)
LCD Projector
and
Screen,
BB/Chalk
Extra reading and Course Books
take home
Bioinformatics: A
assignment
practical guide to
analysis of genes
and proteins and
hand book of
Statistical
genetics