Difference between revisions of "FND-Genetic code"
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Time management: Before you begin, estimate how long it will take you to complete this unit. Then, record in your course journal: the number of hours you estimated, the number of hours you worked on the unit, and the amount of time that passed between start and completion of this unit.
Journal: Document your progress in your Course Journal. Some tasks may ask you to include specific items in your journal. Don't overlook these.
Insights: If you find something particularly noteworthy about this unit, make a note in your insights! page.
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Genetic Code | Genetic Code | ||
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| − | + | (Representing and working with the genetic code) | |
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| − | + | <b>Abstract:</b><br /> | |
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<section begin=abstract /> | <section begin=abstract /> | ||
| − | + | The genetic code is conveniently available as a named character vector, via the | |
| − | + | Biostrings package. We access the code, review syntax of how to work with it, | |
| + | and discuss some of its properties. | ||
<section end=abstract /> | <section end=abstract /> | ||
| − | + | </div> | |
| − | + | <!-- ============================ --> | |
| − | + | <hr> | |
| − | + | <table> | |
| − | == | + | <tr> |
| − | === | + | <td style="padding:10px;"> |
| − | < | + | <b>Objectives:</b><br /> |
| − | <!-- | + | This unit will ... |
| − | You need the following preparation before beginning this unit. If you are not familiar with this material from courses you took previously, you need to prepare yourself from other information sources: | + | * explore the syntax and contents of the named charcater vector that stores the standard genetic code for the Biostrings package; |
| − | < | + | * note the existence of alternative codes; |
| + | * introduce an alternative representation as a 3D array. | ||
| + | </td> | ||
| + | <td style="padding:10px;"> | ||
| + | <b>Outcomes:</b><br /> | ||
| + | After working through this unit you ... | ||
| + | * can fetch and use the genetic code from the Biostrings package; | ||
| + | * solve a variety of tasks concerned with the analysis of the code and its display. | ||
| + | </td> | ||
| + | </tr> | ||
| + | </table> | ||
| + | <!-- ============================ --> | ||
| + | <hr> | ||
| + | <b>Deliverables:</b><br /> | ||
| + | <section begin=deliverables /> | ||
| + | <li><b>Time management</b>: Before you begin, estimate how long it will take you to complete this unit. Then, record in your course journal: the number of hours you estimated, the number of hours you worked on the unit, and the amount of time that passed between start and completion of this unit.</li> | ||
| + | <li><b>Journal</b>: Document your progress in your [[FND-Journal|Course Journal]]. Some tasks may ask you to include specific items in your journal. Don't overlook these.</li> | ||
| + | <li><b>Insights</b>: If you find something particularly noteworthy about this unit, make a note in your [[ABC-Insights|'''insights!''' page]].</li> | ||
| + | <section end=deliverables /> | ||
| + | <!-- ============================ --> | ||
| + | <hr> | ||
| + | <section begin=prerequisites /> | ||
| + | <b>Prerequisites:</b><br /> | ||
| + | You need the following preparation before beginning this unit. If you are not familiar with this material from courses you took previously, you need to prepare yourself from other information sources:<br /> | ||
*<b>Biomolecules</b>: The molecules of life; nucleic acids and amino acids; the genetic code; protein folding; post-translational modifications and protein biochemistry; membrane proteins; biological function. | *<b>Biomolecules</b>: The molecules of life; nucleic acids and amino acids; the genetic code; protein folding; post-translational modifications and protein biochemistry; membrane proteins; biological function. | ||
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*<b>The Central Dogma</b>: Regulation of transcription and translation; protein biosynthesis and degradation; quality control. | *<b>The Central Dogma</b>: Regulation of transcription and translation; protein biosynthesis and degradation; quality control. | ||
| − | + | This unit builds on material covered in the following prerequisite units:<br /> | |
| − | + | *[[RPR-Introduction|RPR-Introduction (Introduction to R)]] | |
| − | *[[RPR-Introduction]] | + | <section end=prerequisites /> |
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| − | + | __TOC__ | |
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=== Evaluation === | === Evaluation === | ||
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<b>Evaluation: NA</b><br /> | <b>Evaluation: NA</b><br /> | ||
| − | :This unit is not evaluated for course marks. | + | <div style="margin-left: 2rem;">This unit is not evaluated for course marks.</div> |
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== Contents == | == Contents == | ||
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| + | {{ABC-unit|FND-Genetic_code.R}} | ||
== Further reading, links and resources == | == Further reading, links and resources == | ||
| − | + | {{#pmid: 8371978}} | |
| − | + | {{#pmid: 21819941}} | |
| − | + | {{#pmid: 28918301}} | |
| − | + | <div class="reference-box">[https://en.wikipedia.org/wiki/Genetic_code '''The Genetic Code''' (Wikipedia)]</div> | |
| − | + | <div class="reference-box">[https://www.ncbi.nlm.nih.gov/Taxonomy/taxonomyhome.html/index.cgi?chapter=tgencodes '''Genetic Code Data''' (NCBI)]</div> | |
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== Notes == | == Notes == | ||
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<div class="about"> | <div class="about"> | ||
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:2017-08-05 | :2017-08-05 | ||
<b>Modified:</b><br /> | <b>Modified:</b><br /> | ||
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<b>Version:</b><br /> | <b>Version:</b><br /> | ||
| − | :0.1 | + | :1.0.1 |
<b>Version history:</b><br /> | <b>Version history:</b><br /> | ||
| + | *1.0.1 2020 Maintenance | ||
| + | *1.0 First live version | ||
*0.1 First stub | *0.1 First stub | ||
</div> | </div> | ||
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{{CC-BY}} | {{CC-BY}} | ||
| + | [[Category:ABC-units]] | ||
| + | {{UNIT}} | ||
| + | {{LIVE}} | ||
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Latest revision as of 22:57, 23 September 2020
Genetic Code
(Representing and working with the genetic code)
Abstract:
The genetic code is conveniently available as a named character vector, via the Biostrings package. We access the code, review syntax of how to work with it, and discuss some of its properties.
|
Objectives:
|
Outcomes:
|
Deliverables:
Prerequisites:
You need the following preparation before beginning this unit. If you are not familiar with this material from courses you took previously, you need to prepare yourself from other information sources:
- Biomolecules: The molecules of life; nucleic acids and amino acids; the genetic code; protein folding; post-translational modifications and protein biochemistry; membrane proteins; biological function.
- The Central Dogma: Regulation of transcription and translation; protein biosynthesis and degradation; quality control.
This unit builds on material covered in the following prerequisite units:
Evaluation
Evaluation: NA
This unit is not evaluated for course marks.
Contents
Task:
- Open RStudio and load the
ABC-unitsR project. If you have loaded it before, choose File → Recent projects → ABC-Units. If you have not loaded it before, follow the instructions in the RPR-Introduction unit. - Choose Tools → Version Control → Pull Branches to fetch the most recent version of the project from its GitHub repository with all changes and bug fixes included.
- Type
init()if requested. - Open the file
FND-Genetic_code.Rand follow the instructions.
Note: take care that you understand all of the code in the script. Evaluation in this course is cumulative and you may be asked to explain any part of code.
Further reading, links and resources
| Ohama et al. (1993) Non-universal decoding of the leucine codon CUG in several Candida species. Nucleic Acids Res 21:4039-45. (pmid: 8371978) |
| Santos et al. (2011) The genetic code of the fungal CTG clade. C R Biol 334:607-11. (pmid: 21819941) |
| Fimmel & Strüngmann (2018) Mathematical fundamentals for the noise immunity of the genetic code. BioSystems 164:186-198. (pmid: 28918301) |
Notes
About ...
Author:
- Boris Steipe <boris.steipe@utoronto.ca>
Created:
- 2017-08-05
Modified:
- 2020-09-23
Version:
- 1.0.1
Version history:
- 1.0.1 2020 Maintenance
- 1.0 First live version
- 0.1 First stub
This copyrighted material is licensed under a Creative Commons Attribution 4.0 International License. Follow the link to learn more.
