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Contents
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Week 1: |
Introduction to the course
Introduction: Biological databases, bioinformatic resources and accessing the biological information
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Week 2: |
Sequence comparison methods: Pairwise sequence alignment, database similarity searching, conservation of amino acids and score matrices |
Week 3: |
Multiple sequence alignment methods and phylogenetic trees |
Week 4: |
Protein families, motifs, patterns; secondary database searching; pattern, motif searching |
Week 5: |
Protein sequence databases: Detailed study of SwissProt/TrEMBL, other sequence databases
Protein domain/family databases: Detailed study of ProDom and DOMO |
Week 6: |
Protein domain/family databases: Detailed study of PROSITE and INTERPRO
Protein structure databases: PDB, MMDB, Swiss-3DIMAGE, etc.; specialized protein databases
Assignment 1 |
Week 7: |
Classification of proteins and prediction of secondary structures |
Week 8: |
Midterm
Evaluation of the exam and solving the exam questions |
Week 9: |
Classification of proteins according to secondary structures: CATH, SCOP |
Week 10: |
Visualisation of the 3D structures of proteins
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Week 11: |
Protein tertiary structure prediction |
Week 12: |
Protein identification and analysis tools: EXPASY server
Assignment 2 |
Week 13: |
Gene and promoter prediction
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Week 14: |
Student project presentation |
Week 15*: |
General Evaluation |
Week 16*: |
Final exam |
Textbooks and materials: |
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Recommended readings: |
1. Essential Bioinformatics. Xiong, J. Cambridge University Press, 2006. 2. Introduction to Bioinformatics. Lesk, A.M. (ed.). Oxford University Press, 2002. 3. Introduction to Bioinformatics: a Theoretical and Practical Approach. Krawetz, S.A. and Womble, D.D. (ed.). Humana Press, Totowa, New Jersey, 2003. 4. Bioinformatics: Genes, Proteins and Computers, Orengo, C.A., Jones, D.T. and Thornton, J.M. Garland Science/BIOS Scientific Publishers, New York, 2003. 5. Bioinformatics: Sequence and Genome Analysis. Mount, D.W. Cold Spring Harbor Laboratory Press; Cold Spring Harbor, USA, 2004. 6. Structural Bioinformatics. Bourne, P.E. and Weissig, H. John Wiley, 2003. 7. Introduction to Protein Architecture: The Structural Biology of Proteins. Lesk, A. M. Oxford University Press, 2001. 8. Introduction to Protein Structure. Branden, C. and Tooze, J. Garland Pub., New York, 1999. |
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* Between 15th and 16th weeks is there a free week for students to prepare for final exam.
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