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MB5522: ADVANCED BIOINFORMATICS AND GENOME SEQUENCING (2019-2020)

Last modified: 25 Sep 2019 09:58


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
Term Second Term Credit Points 15 credits (7.5 ECTS credits)
Campus Aberdeen Sustained Study No
Co-ordinators
  • Dr Elaina Collie-Duguid

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

  • ()
  • Any Postgraduate Programme

What other courses must be taken with this course?

None.

What courses cannot be taken with this course?

None.

Are there a limited number of places available?

No

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.


Contact Teaching Time

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

Teaching Breakdown

More Information about Week Numbers


Details, including assessments, may be subject to change until 30 August 2024 for 1st term courses and 20 December 2024 for 2nd term courses.

Summative Assessments

Class Test - Multiple Choice Questions

Assessment Type Summative Weighting 5
Assessment Weeks 30 Feedback Weeks

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Feedback

MCQ on annotation, gene function and antimicrobial resistance.  Marking and feedback during tuturial

Learning Outcomes
Knowledge LevelThinking SkillOutcome
Sorry, we don't have this information available just now. Please check the course guide on MyAberdeen or with the Course Coordinator

Class Test - Multiple Choice Questions

Assessment Type Summative Weighting 5
Assessment Weeks 28 Feedback Weeks

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Feedback

MCQ on genome assembly process, outputs, and caveats. Marking and feedback during tutorial.

Learning Outcomes
Knowledge LevelThinking SkillOutcome
Sorry, we don't have this information available just now. Please check the course guide on MyAberdeen or with the Course Coordinator

Class Test - Multiple Choice Questions

Assessment Type Summative Weighting 10
Assessment Weeks 26 Feedback Weeks

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Feedback
Learning Outcomes
Knowledge LevelThinking SkillOutcome
Sorry, we don't have this information available just now. Please check the course guide on MyAberdeen or with the Course Coordinator

Oral Presentation: Individual

Assessment Type Summative Weighting 15
Assessment Weeks 31 Feedback Weeks 32

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Feedback

Students will give a 12 minute oral presentation on a specified topic in microbial genomics, followed by 5 minutes of questions during which feedback will be provided.  Further feedback will be provided within the marking rubric in MyAberdeen.

Learning Outcomes
Knowledge LevelThinking SkillOutcome
Sorry, we don't have this information available just now. Please check the course guide on MyAberdeen or with the Course Coordinator

Report: Individual

Assessment Type Summative Weighting 65
Assessment Weeks 33 Feedback Weeks 35

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Feedback
Learning Outcomes
Knowledge LevelThinking SkillOutcome
Sorry, we don't have this information available just now. Please check the course guide on MyAberdeen or with the Course Coordinator

Formative Assessment

There are no assessments for this course.

Course Learning Outcomes

Knowledge LevelThinking SkillOutcome
ConceptualApplyUnderstand Next Generation Sequencing (NGS) technologies and data, and its application
ProceduralAnalyseBasic skills in Unix/Command line and using a High Performance Compute Cluster
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.
ProceduralCreateDevelop analytical and critical skills in microbial genomics

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