COMP40400 Bioinformatics

Academic Year 2021/2022

-Proteins. DNA. RNA. Public molecular biology repositories. -Dynamic programming algorithms for sequence comparison: global sequence alignment (Needleman-Wunsch); local sequence alignment (Smith-Waterman); semiglobal comparison. Variations to the basic alignment algorithms: variable gab penalties; KBand; substitution matrices. BLAST. -Multiple sequence alignments. ClustalW. -Introduction to molecular phylogenetics. Methods for tree reconstruction: distance-based methods (UPGMA, Neighbour-Joining); maximum parsimony; maximum likelihood and full bayesian; bootstrapping. -Introduction to protein structure prediction. Introduction to artificial neural networks. Protein structure prediction by machine learning: 1D structural features; 2D structural features; 3D reconstruction.

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Curricular information is subject to change

Learning Outcomes:

At the end of the course students should: -be aware of most of the main goals and problems in computational biology; -understand dynamic programming techniques and be able to replicate at least manually the main dynamic programming techniques for biological sequences; -be familiar with the main public molecular biology databases ; -understand the goals of molecular phylogeny, and be aware of the main techniques proposed to compute phylogenies; -understand the basic concepts of protein structure prediction

Student Effort Hours: 
Student Effort Type Hours
Autonomous Student Learning








Approaches to Teaching and Learning:
Individual completion of practical bioinformatics tasks. 
Requirements, Exclusions and Recommendations

Not applicable to this module.

Module Requisites and Incompatibles
Not applicable to this module.
Assessment Strategy  
Description Timing Open Book Exam Component Scale Must Pass Component % of Final Grade
Assignment: Protein structure prediction assignment Week 10 n/a Graded No


Assignment: Public tools and databases assignment Week 8 n/a Graded No


Assignment: Phylogeny assignment Week 6 n/a Graded No


Examination: final exam, two hours 2 hour End of Trimester Exam No Graded No


Assignment: Dynamic programming assignment Week 3 n/a Graded No


Carry forward of passed components
Resit In Terminal Exam
Autumn No
Please see Student Jargon Buster for more information about remediation types and timing. 
Feedback Strategy/Strategies

• Feedback individually to students, post-assessment

How will my Feedback be Delivered?

Not yet recorded.

Timetabling information is displayed only for guidance purposes, relates to the current Academic Year only and is subject to change.
Lecture Offering 1 Week(s) - 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32 Thurs 14:00 - 14:50