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CMPSMB4Y - FUNDAMENTALS OF COMPUTATIONAL AND STRUCTURAL GENOMICS

Module Code:
CMPSMB4Y
Department:
Computing Sciences
Credit Value:
30
Level:
M
The initial section of the module will revise biological aspects of genomic information, gene and genome evolution. Examples will be worked through for evaluating sequence data and to recognise problems of sequence data analyses. Gene annotation and gene searching procedures will be introduced and approaches for phylogenetic analyses will also be covered. Following that, sequence alignment and sequence recognition protocols will be investigated and algorithms for this purpose will be examined. Understanding of the experimental techniques used to determine protein structure will be explained and in particular emphasis is paid to the detection of errors in these structures. From there methods used to predict protein structures will be covered. These will include secondary structure prediction, fold recognition (threading) and homology modelling. Some of the methods introduced earlier, such as profiles, will reappear in the context of structure prediction so consolidating understanding of these concepts. In addition the methods of molecular mechanics will be presented together with a general introduction to protein dynamics.

Reading:

  • Gaur D. & Li W.H Fundamentals of Molecular Evolution, (Sinauer Associates Inc.(2000)
  • Lodish, H., Berk, A., Zipursky, S.L., Matsudaira, P. Molecular Cell Biology 4th Edition, W H Freeman Co.(1999)
  • Attwood, T.K. & Parry-Smith, D.J. Introduction to Bioinformatics, Addison Wesley Longman ISBN 0 582 327881. (1999)
  • Durbin, R, Eddy S., Krogh A., Mitchison G, Biological Sequence Analysis,Cambridge.
  • T.E. Creighton, Proteins: Structures and Molecular Properties,,2nd Edition (Freeman)
  • C. Brandon and J. Tooze, Introduction to Protein Structure, (2nd edition, Garland)
  • Arthur M. Lesk, Introduction to Protein Architecture, (Oxford)
    (Other texts and literature references may be recommended during the course of the unit)

Submission:

Written coursework should be submitted by following the standard CMP practice. Students are advised to refer to the Guidelines and Hints on Written Work in CMP.

Deadlines:

If coursework is handed in after the deadline day or an agreed extension:

Work submitted Marks deducted
After 15:00 on the due date and before 15:00 on the day following the due date 10 marks
After 15:00 on the second day after the due date and before 15:00 on the third day after the due date 20 marks
After 15:00 on the third day after the due date and before 15:00 on the 20th day after the due date.  All the marks the work merits if submitted on time (ie no marks awarded) 
After 20 working days Work will not be marked and a mark of zero will be entered


Saturdays and Sundays will NOT be taken into account for the purposes of calculation of marks deducted.

All extension requests will be managed through the LTS Hub. A request for an extension to a deadline for the submission of work for assessment should be submitted by the student to the appropriate Learning and Teaching Service Hub, prior to the deadline, on a University Extension Request Form accompanied by appropriate evidence. Extension requests will be considered by the appropriate Learning and Teaching Service Manager in those instances where (a) acceptable extenuating circumstances exist and (b) the request is submitted before the deadline. All other cases will be considered by a Coursework Coordinator in CMP.

For more details, including how to apply for an extension due to extenuating circumstances download Submission for Work Assessment (PDF, 39KB)
 

Plagiarism:

Plagiarism is the copying or close paraphrasing of published or unpublished work, including    the work of another student; without due acknowledgement. Plagiarism is regarded a serious offence by the University, and all cases will be investigated. Possible consequences of plagiarism include deduction of marks and disciplinary action, as detailed by UEA's Policy on Plagiarism and Collusion.


 


Module specific:

  • Have acquired knowledge of biological aspects of genomic information, gene and genome evolution
  • Obtained experience in evaluating sequence data and understand some of the pitfalls in analyses
  • Have an understanding of sequence alignment and sequence pattern recognition protocols
  • Gained experience with the use of gene alignment and pattern recognition algorithms and prepared your own algorithm for this purpose
  • Have an appreciation of how techniques such as X-ray crystallography and NMR spectroscopy are used to determine macromolecular structures
  • Have a knowledge of the principles of protein structure and of the major domain structural classes
  • Have a knowledge of protein fold recognition methods such as threading
    understand how sequence alignments and homology modelling can be used to derive structural models of proteins
  • Have an appreciation of molecular mechanics force fields and how they are used in energy minimisation, normal mode analysis and molecular dynamics simulations

Transferable skills:

  • Improved programming skills
  • Better ability to understand methods and algorithms

  • Confidence in understanding of the basics of computational biology.
  • Critical approach to commonly used computational biology software.

Two lectures a week plus lab sessions

Total hours: 54

Lectures: 30 hours; (with provisional weekly schedule)

  1. Gene and Genomic Structure
  2. Gene and Genomic Evolution
  3. Understanding and Assessing Problems in Sequence Data Analyses
  4. Dot Plots
  5. Pairwise Alignment
  6. Searching Databases using Pairwise Alignment
  7. Multiple-Alignment
  8. Profiles
  9. PSI-BLAST
  10. Hidden-Markoff Models, Pfam
  11. Motifs and the PROSITE database
  12. Protein X-ray crystallography
  13. Protein nuclear magnetic resonance
  14. Protein structure at its various levels
  15. Secondary structure prediction
  16. Structure alignment and comparison
  17. Fold recognition
  18. Homology modelling
  19. Protein flexibility
  20. Molecular mechanics

Workshops: 0 hours

Laboratory work: 24 hours


Coursework 100%;

Four pieces of coursework: 20%, 30%, 30%, 20%.