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COMPUTATIONAL BIOLOGY
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Course |
Learning outcomes (at course level) |
Learning and teaching strategies |
Assessment Strategies |
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Paper Code |
Paper Title |
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ZOL 121 |
Biosystematic, Taxonomy & Evolution |
The students will be able to-
CO1:Examine various techniques used in biological sciences. CO2: Develop the functioning and applications of various types of Microscopic techniques. CO3: Verify the working principles, instrumentation and implement the use of various analytical instruments like centrifugation, spectrophotometer, pH meter, Chromatography, Electrophoresis and PCR. CO4: Appraise about the concepts of bioinformatics and its applications, retrieve information from biological databases along with the submission of sequences into the databases and will use general computational tools to solve research problems. |
Approach in teaching: Interactive Lectures, Discussion, Tutorials, Reading assignments, Demonstration, Team teaching
Learning activities for the students: Self-learning assignments, Effective questions, Simulation, Seminar presentation, Giving tasks, Field practical |
Class test Semester end examinations, Quiz Assignments Presentation Individual and group projects |
Biological Databases
Introduction to biological databases;
Primary, secondary and composite databases;
Nucleic acid databases (GenBank, DDBJ, EMBL and NDB);
Protein databases (PIR, SWISS-PROT, TrEMBL, PDB);
Metabolic pathway database (KEGG, EcoCyc, and MetaCyc);
Small molecule databases (PubChem, Drug Bank, ZINC, CSD)
Basic Concepts of Sequence Alignment
Scoring Matrices (PAM, BLOSUM),
Methods of Alignment (Dot matrix, Dynamic Programming, BLAST and FASTA);
Local and global alignment, pairwise and multiple sequence alignments; Similarity, identity and homology of sequences.
Sequence file format (flat file, FASTA, GCG, EMBL, Clustal, Phylip, Swiss-Prot); Sequence
Annotation; Data retrieval systems (SRS, Entrez)
Microscopy
Magnification and Resolving Power
Light (bright-field, dark-field and phase contrast)
Electron (SEM and TEM)
Spectrophotometer (UV- Visible)
Principles and use of analytical instruments:
Centrifugation (Density and Differential)
Chromatography (Paper and TLC)
Electrophoresis (Agarose and PAGE)
PCR
Introduction, scope and application of Biostatistics
Frequency distribution
Graphical presentation of data (bar diagram, frequency polygon, histogram, pie chart)
Mean. mode, median and their significance
Standard deviation
ESSENTIAL READINGS:
● Essential Bioinformatics, JinXiong, John Wiley and Sons. 2006.
● Introduction to Bioinformatics, A Teresa and D P Smith, Prentice Hall, 1999.
● Statistical Methods in Biology, N T J Bailey, Cambridge University Press, 1995.
● Statistics for Biologist, R C Campbell, Cambridge University Press, 1989.
● Bioinformatics, A practical Guide to the Analysis of Genes and Proteins, (2nd edition), AD Baxevanis, and B F Ouellette, John Wiley and Sons, 2002.
● Introduction to instrumental analysis-Robert Braun-McGraw Hill.
● A biologist Guide to principles and Techniques of Practical Biochemistry-K, Wilson and
K.H. GouldingElBSEdn.
● Essentials of Biophysics, P Narayanan, New Age Int. Pub. New Delhi. 2000.
● Clark &Swizer. Experimental Biochemistry. Freeman, 2000.
● Principles and Practice of Bioanalysis, R F Venn, Taylor and Francis, 2003.
● Locquin and Langeron. Handbook of Microscopy. Butterwaths, 1983.
SUGGESTED READINGS:
● Fundamentals of Biostatistics, Khan, Publishing Corporation, 1999
● Biostatistics: A Foundation for Analysis in Health Sciences, (6th edition), W W Daniel,
John Wiley and Sons Inc., 1995.
● Instant notes, Bioinformatics, Westhead, Parish, and Twyman, (1stedition), Bios Scientific
Publishers Ltd., 2003.
● Introduction to Bioinformatics, A M Lesk, Oxford University Press, 2002.
● Molecular databases for Protein sequence and Structure studies, J A Sillince and M Sillince, Springer Verlag, 1991
● Practical statistics for Experimental Biologists, A C Swardlaw, John Wiley and sons Inc.,
1985
● Sequence Analysis Primer, Gribskov and Devereux, Stockton Press, 1989
● David W. Mount's "Bioinformatics" [Cold Spring Harbor Press; ISBN 0879697121].
● James Tisdall. Beginning Perl for Bioinformatics An Introduction to Perl for Biologists.
Publisher: O'Reilly Media. October 2001.
e-RESOURCES:
● e- PGPathshala
=https://epgp.inflibnet.ac.in/Home/ViewSubject?catid=2rAs1Puvga4LW93zMe83...
● https://www.ncbi.nlm.nih.gov/
● https://vlab.amrita.edu/index.php?sub=3&brch=311
JOURNALS:
● Journal of Bioinformatics and Computational Biology. ISSN (print): 0219-7200 | ISSN
(online): 1757-6334.
● BMC Bioinformatics, Publisher: BioMed Central ltd. ISSN: 1471-2105.
