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BIO8211 Bioinformatics

Semester 2, 2013 On-campus Toowoomba
Units : 1
Faculty or Section : Faculty of Sciences
School or Department : Biological & Physical Sciences
Version produced : 23 April 2014

Contents on this page

Staffing

Examiner: Guang Liu
Moderator: Grant Daggard

Requisites

Co-requisite: BIO2209

Rationale

Bioinformatics brings together the fields of life science, computer science and statistics. Bioinformaticians are involved in the development of technologies for storing, extracting, organizing, analysing, interpreting and utilizing biological information. With the ever increasing size of genome and other biological data sets, students are required to extend their knowledge of existing statistical methodologies to the analysis of huge amount of data. Students of bioinformatics gain a better understanding of biological systems by creative application of statistics and computer analysis. Cross-disciplinary knowledge courses are essential to the development of this emerging discipline.

Synopsis

You will be introduced in an integrated approach to the cross-disciplinary field of Bioinformatics. This course provides an introduction to both theoretical and practical aspects of DNA and protein sequence analysis including the searching of DNA, protein and nucleic acid databases using homology-based and pattern-based search algorithms, as well as sequence comparisons and alignments and evolutionary analysis. You will develop skills in interfacing with and retrieving information from sequence and genome databases. Methods of sequence alignment including dynamic programming and the supporting statistical theory are introduced. Topics include collection of sequences, sequence alignment, prediction of RNA secondary structure, phylogenetic relationships, gene prediction and protein structure prediction.

Objectives

On completion of this course students will be able to:

  1. Outline basic molecular tools involved in DNA analysis (e.g. sequencing) which underpin or support bioinformatics based analysis;
  2. Conduct database analyses at the DNA, RNA and protein level;
  3. Predict molecular structures from genomic information including: promoters,open reading frames (introns, exons), genes and predicted protein structures;
  4. Be able to input data into and, interpret output from, a range of bioinformatics software tools (a focus being on widely available web-based packages);
  5. Analyse gene homology and predict evolutionary relationships;
  6. Show a high level of skill in the use of informatics techniques with an emphasis on the organisation, display and interrogation of complex data;
  7. Understand the limitations of existing techniques.

Topics

Description Weighting(%)
1. Review of DNA structure and organisation 10.00
2. Bioinformatics: collecting and assessing genome related data. An historical perspective including the development of public databases and related internet resources. 5.00
3. Review of basic molecular tools that may be used to generate bioinfomatics related data (e.g. Southern Analysis, DNA sequencing) 10.00
4. Database searching (e.g. FASTA and BLAST algorithms) 15.00
5. Sequence alignment - pairs, multiple sequence alignment and identifying similar sequences including basic statistical approaches (e.g PAM and BLOSUM index) 20.00
6. Genome analysis including gene prediction and identification 15.00
7. Protein classification, structure and prediction 15.00
8. Phylogenetic relationships 10.00

Text and materials required to be purchased or accessed

ALL textbooks and materials available to be purchased can be sourced from USQ's Online Bookshop (unless otherwise stated). (https://bookshop.usq.edu.au/bookweb/subject.cgi?year=2013&sem=02&subject1=BIO8211)

Please contact us for alternative purchase options from USQ Bookshop. (https://bookshop.usq.edu.au/contact/)

  • Zvelebil, M & Baum JO 2008, Understanding Bioinformatics, Garland Science.
    (ISBN 0 81 534024 9.)

Reference materials

Reference materials are materials that, if accessed by students, may improve their knowledge and understanding of the material in the course and enrich their learning experience.
  • Baxevanis, AD & Ouellette, BFF 2005, Bioinformatics: A practical guide to the analysis of genes and proteins, 3rd edn, Wiley-Liss.
    (ISBN 0471478784.)
  • Brown, TA 2007, Genomes 3, GS Garland Science, New York.
    (0 8153 4138 5.)
  • Higgins, D & Taylor, W 2000, Bioinformatics: sequence, structure and databanks: a practical approach, Oxford University Press, Oxford.
    (ISBN 0 19 963790 3.)
  • Krane, DE & Raymer, ML 2003, Fundamental concepts of bioinformatics, Benjamin Cummings, San Francisco.
    (ISBN 0 8053 4633 3.)
  • Lee, Mei-Ling 2004, Analysis of microarray gene expression data, Kluwer Academic Publishers, Boston.
    (ISBN 0-7923-7087-2.)
  • Mount, DW 2004, Bioinformatics: sequence and genome analysis, 2nd edn, Cold Spring Harbour Laboratory Press, New York.
  • Wong, L (ed) 2004, The practical bioinformatician, World Scientific Publishing, Singapore.
    (ISBN 981-238-846-X.)

Student workload requirements

Activity Hours
Assessments 40.00
Examinations 2.00
Online Lectures 26.00
Private Study 73.00
Tutorials 26.00

Assessment details

Description Marks out of Wtg (%) Due Date Notes
ASSIGNMENT 1 20 20 16 Jul 2013 (see note 1)
ASSIGNMENT 2 20 20 16 Jul 2013 (see note 2)
2HR RESTRICTED EXAM 100 60 End S2 (see note 3)

NOTES
  1. Examiner to advise due date for Assignment 1.
  2. Examiner to advise due date for Assignment 2
  3. Examination dates will be available during the Semester. Please refer to the examination timetable when published.

Important assessment information

  1. Attendance requirements:
    It is the students' responsibility to attend and participate appropriately in all activities (such as lectures, tutorials, laboratories and practical work) scheduled for them, and to study all material provided to them or required to be accessed by them to maximise their chance of meeting the objectives of the course and to be informed of course-related activities and administration.

  2. Requirements for students to complete each assessment item satisfactorily:
    To satisfactorily complete an assessment item a student must achieve at least 50% of the marks or a grade of at least C-. Students do not have to satisfactorily complete each assessment item to be awarded a passing grade in this course. Refer to Statement 4 below for the requirements to receive a passing grade in this course.

  3. Penalties for late submission of required work:
    If students submit assignments after the due date without (prior) approval of the examiner then a penalty of 5% of the total marks gained by the student for the assignment may apply for each working day late up to ten working days at which time a mark of zero may be recorded. No assignments will be accepted after model answers have been posted.

  4. Requirements for student to be awarded a passing grade in the course:
    To be assured of receiving a passing grade a student must achieve at least 50% of the total weighted marks available for the course.

  5. Method used to combine assessment results to attain final grade:
    The final grades for students will be assigned on the basis of the aggregate of the weighted marks obtained for each of the summative assessment items in the course.

  6. Examination information:
    Candidates are allowed access only to specific materials during a Restricted Examination. The only materials that candidates may use in the restricted examination for this course are: writing materials (non-electronic and free from material which could give the student an unfair advantage in the examination); calculators which cannot hold textual information (students must indicate on their examination paper the make and model of any calculator(s) they use during the examination). Students whose first language is not English, may, take an appropriate unmarked non-electronic translation dictionary (but not technical dictionary) into the examination. Dictionaries with any handwritten notes will not be permitted. Translation dictionaries will be subject to perusal and may be removed from the candidate's possession until appropriate disciplinary action is completed if found to contain material that could give the candidate an unfair advantage.

  7. Examination period when Deferred/Supplementary examinations will be held:
    Any Deferred or Supplementary examinations for this course will be held during the next examination period.

  8. University Student Policies:
    Students should read the USQ policies: Definitions, Assessment and Student Academic Misconduct to avoid actions which might contravene University policies and practices. These policies can be found at http://policy.usq.edu.au.

Assessment notes

  1. Students must retain a copy of any assignment submitted. If requested, students will be required to provide a copy of assignments submitted for assessment purposes. Such copies should be despatched to USQ within 24 hours of receipt of a request being made.

  2. Harvard (AGPS) is the referencing system required in this course. Students should use Harvard (AGPS) style in their assignments to format details of the information sources they have cited in their work. The Harvard (AGPS) style to be used is defined by the USQ Library's referencing guide. http://www.usq.edu.au/library/referencing