Last modified: 25 Sep 2019 09:58
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.
| Study Type | Postgraduate | Level | 5 |
|---|---|---|---|
| Session | Second Sub Session | Credit Points | 15 credits (7.5 ECTS credits) |
| Campus | Aberdeen | Sustained Study | No |
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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.
Information on contact teaching time is available from the course guide.
| Assessment Type | Summative | Weighting | 5 | |
|---|---|---|---|---|
| Assessment Weeks | 30 | Feedback Weeks | ||
| Feedback |
MCQ on annotation, gene function and antimicrobial resistance. Marking and feedback during tuturial |
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| Knowledge Level | Thinking Skill | Outcome |
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| Assessment Type | Summative | Weighting | 5 | |
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| Assessment Weeks | 28 | Feedback Weeks | ||
| Feedback |
MCQ on genome assembly process, outputs, and caveats. Marking and feedback during tutorial. |
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| Knowledge Level | Thinking Skill | Outcome |
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| Assessment Type | Summative | Weighting | 10 | |
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| Assessment Weeks | 26 | Feedback Weeks | ||
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| Knowledge Level | Thinking Skill | Outcome |
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| Assessment Type | Summative | Weighting | 15 | |
|---|---|---|---|---|
| Assessment Weeks | 31 | Feedback Weeks | 32 | |
| 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. |
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| Knowledge Level | Thinking Skill | Outcome |
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| Assessment Type | Summative | Weighting | 65 | |
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| Assessment Weeks | 33 | Feedback Weeks | 35 | |
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| Knowledge Level | Thinking Skill | Outcome |
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There are no assessments for this course.
| Knowledge Level | Thinking Skill | Outcome |
|---|---|---|
| Conceptual | Apply | Understand Next Generation Sequencing (NGS) technologies and data, and its application |
| Procedural | Analyse | Basic skills in Unix/Command line and using a High Performance Compute Cluster |
| Procedural | Evaluate | Assemble a bacterial genome using a web-based platform and using the command line, and evaluate assembly quality |
| Procedural | Create | Annotate a bacterial genome and use biological databases to gain insight into gene functions. |
| Procedural | Create | Develop analytical and critical skills in microbial genomics |
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