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bioinformatics

The Z-405 Bioinformatics course aims to introduce students to the fundamental concepts, databases, and tools used in bioinformatics. Upon completion, students will be able to explain bioinformatics basics, utilize search tools, and perform data retrieval and analysis. The course includes practical tutorials, assessments, and a variety of reference materials to support learning.

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35 views3 pages

bioinformatics

The Z-405 Bioinformatics course aims to introduce students to the fundamental concepts, databases, and tools used in bioinformatics. Upon completion, students will be able to explain bioinformatics basics, utilize search tools, and perform data retrieval and analysis. The course includes practical tutorials, assessments, and a variety of reference materials to support learning.

Uploaded by

emaan waris
Copyright
© © All Rights Reserved
We take content rights seriously. If you suspect this is your content, claim it here.
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Z-405 BIOINFORMATICS Cr.

3(1+2)
Course Objectives
The course will provide:
1. An Introduction to Bioinformatics.
2. To develop awareness about Fundamental Bioinformatics Databases.
3. Information on the tools used to compute solutions to those problems, and the theory upon which
those tools are based.

Course Outcomes:
Upon successful completion of the course, the students should be able to:
1) GAIN an understanding of the basic concepts of Bioinformatics.
2) EXPLAIN the basics of bioinformatics and computational biology.
3) USE bioinformatics search tools on the internet for mining data, pairwise and multiple sequence
alignments and predict protein structures.

Course Contents:
1) Introduction:
• Introduction to Bioinformatics,
• Scope of Bioinformatics, useful websites
• Aims of Bioinformatics, disciplines related to Bioinformatics, major tasks involved in
bioinformatics analysis, bio-informatics tools
• Human genome project
2) Biological databases
• Data and types of data, data acquisition
• Major DNA databases around the world, NCBI, BOLD, DDBJ
• Major protein databases in the world, protein sequence databases, protein structure databases
• Specialized databases, genome and organism databases
• Non sequence databases, pubmed, pubmed health, OMIM
3) Genome mapping
• Genetic and linkage mapping, physical mapping
4) Gene family:
• Introduction, types, protein family, Globin family as an example, globin genes and chains,
evolution of globin proteins in human, combination and types of globin proteins in human.
5) Data Retrieval:
• Searching sequence databases
• FASTA format
• retrieval of nucleotide sequence data, retrieval of protein sequence and structure data, retrieval of
literature and map data
6) Primer Designing:
• Primer and probe, qualities of primer, general rules for primer designing
• Websites used for primer designing
7) Sequence Alignment:
• Importance and significance of alignment, methods for sequence alignment
• Local and global alignment, pair-wise local alignment
8) BLAST:
• Introduction, types, uses, algorithm, BLAST Scores
9) Multiple Sequence Alignment:
• Introduction, tools for MSA, uses and importance
10) Phylogenetic analysis:
• Introduction, interpretation, rooted and unrooted tree,
• phylogenetic methods, tree terminology, comparison of methods, software

Practicals/Tutorials:
• Introduction to NCBI
• Retrieving Literature from NCBI
• Classification of an organism using NCBI
• Retrieving FASTA sequence for nucleotide and protein
• Retrieving disease gene information
• Searching gene families
• Primer Designing
• BLASTing a nucleotide / amino acid sequence
• Multiple Sequence Alignment using different amino acids / nucleotide sequences
• Phylogenetic Analysis of different nucleotide / amino acid sequences
• Microarrays data retrieval from the web

Teaching-Learning Strategies
Teaching will be a combination of class lectures, class discussions, and group work. Short
videos/films will be shown on occasion.

Assignments
The sessional work will be a combination of written assignments, class quizzes, presentation, and
class participation/attendance.

Assessments and Examination


Sessional Work: 25 marks
Midterm Exam: 35 marks
Final Exam: 40 marks

Text and Reference Books:


1. Baxevanis, A.D., Ouellette, B.F.F. (2011) Bioinformatics: A Practical Guide to the Analysis of
Genes and Proteins. John Wiley & sons,Inc.
2. Rastogi, S.C., Mendiratta, N., Rastogi, P. (2011) Bioinformatics Methods and Applications:
Genomics, Proteomics and Drug Discovery. PHI publishing.
3. Pevsner, J. (2015) Bioinformatics and Functional Genomics. 3rd Edition. Willey-Blackwell
4. Lesk, A. (2014) Introduction to Bioinformatics. 4th Edition. Oxford University Press
5. Selzer, P., Marhofer, R. and Rohwer, A. (2008) Applied Bioinformatics: An Introduction. Springer
publishing, Germany.
6. Primerose, S.B. (2004) Genomics: Applications in Human Biology. Willey- Blackwell
7. Westhead, D.R., Parish, J.H., Twyman, R.M. (2003) Instant Notes on Bioinformatics. Viva Books
Private Limited.
8. Krane, D.E. and Raymer, M.L. (2002) Fundamental Concepts of Bioinformatics. Benjamin
Cummings.
9. Gibas, C. and Jambeck, P. (2001) Developing Bioinformatics Computer Skills. O’Reilly
publishers.

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