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Last modified: 22 Oct 2021 09:20

Course Overview

An exciting course that brings a student right up to date with bioinformatics, genome assembly and annotation technology. You, the student, will isolate a novel bacterium from the environment and purify its DNA. This will be whole genome sequenced, and you will then assemble your own bacterial genome and functionally annotate it, taught by expert bioinformaticians from our Centre for Genome-Enabled Biology and Medicine. Your analysis will enable you to identify the species you have isolated, its metabolic and environmental responses, growth constraints and regulation, cell surface markers and antibiotic resistance, producing a full inventory of genes and their presumptive functions. Overall the course prepares a student for future employment in a biosciences workplace where genome sequencing and annotation is becoming an everyday tool of modern biotechnology.

Course Details

Study Type Postgraduate Level 5
Session Second Sub Session Credit Points 15 credits (7.5 ECTS credits)
Campus Aberdeen Sustained Study No
  • Dr E Collie-duguid

What courses & programmes must have been taken before this course?

  • Either () or Master Of Science In Industrial Biotechnology
  • Any Postgraduate Programme

What other courses must be taken with this course?


What courses cannot be taken with this course?


Are there a limited number of places available?


Course Description

This course will take students through the exciting and challenging process of analysing the sequence of a bacterial genome from an isolate that they themselves have identified and purified DNA from in semester 1. The course will teach students how to quality filter and trim raw sequencing data, assemble a genome, quality control the output, annotate genes, and carry out functional gene analysis using modern bioinformatics, to produce an assembled genome and full inventory of the genes of a novel bacterial isolate. This course will develop your knowledge and skills in bioinformatics analysis of genomic data and you will learn how to use scripting via the command line and the Galaxy interface.

Students wishing to assemble and annotate the genome of a bacterial isolate that they have isolated and extracted DNA from themselves must take Biotechnology BT5014, where this will be performed in a laboratory practical in semester 1. However, BT5014 is not a mandatory pre-requisite for this course and if you have not studied BT5014, bacterial genome raw sequencing reads will be provided to you to use for assembly and annotation in MB5522.

In light of Covid-19 this information is indicative and may be subject to change.

Contact Teaching Time

Information on contact teaching time is available from the course guide.

Teaching Breakdown

  • 1 Computer Practical during University weeks 27 - 31, 33
  • 2 Computer Practicals during University week32
  • 1 Seminar during University week27
  • 1 Tutorial during University weeks 26, 34

More Information about Week Numbers

In light of Covid-19 and the move to blended learning delivery the assessment information advertised for second half-session courses may be subject to change. All updates for second-half session courses will be actioned in advance of the second half-session teaching starting. Please check back regularly for updates.

Summative Assessments

Coding test (short answer test) (15 %)  

Short answer test (15 %)  

Course blog (5 %)  

3500 word Report (65 %) 

Resit for students taking the course in AY20/21:

Resit (viva) will assess understanding of the learning outcomes of the course, does not cover individual assignments.

Formative Assessment

3 x MCQ – formative (0%)  


Course Learning Outcomes

Knowledge LevelThinking SkillOutcome
ProceduralEvaluateAssemble a bacterial genome using a web-based platform and using the command line, and evaluate assembly quality
ProceduralCreateAnnotate a bacterial genome and use biological databases to gain insight into gene functions.
ConceptualApplyUnderstand Next Generation Sequencing (NGS) technologies and data, and its application
ProceduralCreateDevelop analytical and critical skills in microbial genomics
ProceduralAnalyseBasic skills in Unix/Command line and using a High Performance Compute Cluster

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