Bio informatics
Course code:
Course Level:
Course Credit:
MBC 7202
1
2 CU
Brief Course Description
This course starts with introduction to Bioinformatic, what it can and why it is now very
important. This will be followed by introduction to DNA databases (NCBI, EMBL, DDBJ),
Protein databases (GenPept, TrEMBL, Swiss Prot, PIR, ExPasy, SMART, etc). Search tools for
data retrieval (Entrenz, DBGET, PubMed), Sequence alignment soft ware programmes (BLAST,
FASTA, etc), Sequence alignment types. Main sequence types (mRNA, cDNA, genomic DNA
ESTs, GSS) and end with Phylogenic analysis and Structural modelling.
Course Objectives
At the end of this course learners should be able to:
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Define bioinformatics and explain what it can do
Describe the various DNA and Protein databases.
Explain the principles search tools for data retrieval
Explain soft ware programmes available for sequence alignments
Explain the sequence alignment types
Describe the main sequence types.
Explain Phylogenic analysis and structural modelling.
Course outline
Concept of bioinformatics
(6 hours)
Definition of bioinformatics, what it can do, and how it has influenced research. Different
Nucleic acid databases such as the National Centre for Biotechnology Information (NCBI),
European Molecular Biology Laboratory (EMBL), DNA Data Bank of Japan (DDJ), and
GeneBank store DNA sequences. Search tools for retrieval of data namely: Sequence Retrieval
System (SRS), Entrez and DBET will be explained and demonstrated using Internet.
Soft ware programmes available for sequence alignments
(6 hours)
The practical use of software programmes (BLAST, FASTA, etc) for sequence alignments
Will be demonstrated using a computer connected to the internet, sequence alignment types such
as Local sequence alignment, Global sequence alignment and multiple sequence alignment will
be explained.
Main sequence types in the GenBanks
(3 hours)
Main sequence types in the GenBanks are mRNA, cDNA, genomic DNA ESTs and GSS will be
explained. The course will end with Phylogenic analysis and Structural modeling.
Tutorials
(10 hours)
Practical
(20 hours)
Mode of course delivery
This course will be conducted in three main ways involving formal lectures, practical
Assignments using computers/Coursework, and Presentations.
Assessment
Assessment will be by examination, tests, assignments reports, and presentations. Their relative
contribution to the final grade is shown below:
Requirement
Assignments and presentations
Tests
Final examination
Total
Contribution
20 %
20 %
60 %
100 %
Reading List
1. Bioinformatics, A Practical Guide to the Analysis of Genes and Proteins.
Second edition, A john Wiley & sons, InC., Publications
Edited by Andreas D. Baxevanis and B.F.Francis Ouellette
2. NCBI databases and tools http://www.ncbi.nlm.nih.gov
3. BLAST
http://www.ncbi.nlm.nih.gov/BLAST/
4.ENTREZ http://www.ncbi.nlm.nih.gov/Entrez/