Fundamentals of Computational and Structural Genomics

Overview

The module starts with recalling biological aspects of genomic information, gene and genome evolution. This is followed by an introduction of fundamental concepts and algorithms underpinning high-throughput sequencing/sequence assembly, sequence alignment, and analysis of genetic variance. This also includes a discussion of the most popular tools used for these purposes. In addition, fundamentals of protein structure will be introduced and some of the methods for structural bioinformatics will be discussed. Wherever appropriate, examples will be worked through.

Objectives

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

Learning Outcomes

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

Library Resources

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)

Teaching Approach

Two lectures a week plus lab sessions

Total hours: 54

Lectures: 30 hours; (with provisional weekly schedule)

Gene and Genomic Structure
Gene and Genomic Evolution
Understanding and Assessing Problems in Sequence Data Analyses
Dot Plots
Pairwise Alignment
Searching Databases using Pairwise Alignment
Multiple-Alignment
Profiles
PSI-BLAST
Hidden-Markoff Models, Pfam
Motifs and the PROSITE database
Protein X-ray crystallography
Protein nuclear magnetic resonance
Protein structure at its various levels
Secondary structure prediction
Structure alignment and comparison
Fold recognition
Homology modelling
Protein flexibility
Molecular mechanics

Workshops: 0 hours

Laboratory work: 24 hours

Method Of Assessment

Coursework 100%;

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

Conventions And Standards

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

Coursework should be submitted before 23:59 on the deadline day. Paper copies can be submitted via the Hub drop boxes up to 22.00 in the LTS Hub, and there will be a ‘late box’ in the Library for submissions between 22.00 and midnight.

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

Work submitted	Marks deducted
On the day following the due date	10 marks
On either the 2nd or 3rd day after the due date	20 marks
On the 4th day after the due date and before 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

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.

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 anddisciplinary action, as detailed by UEA's Policy on Plagiarism and Collusion.

UEA

Courses

Fundamentals of Computational and Structural Genomics (CMPSMB4Y-A-YEAR)