Difference between revisions of "FND-Genetic code"

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<div style="padding:5px; border:1px solid #000000; background-color:#b3dbce; font-size:300%; font-weight:400; color: #000000; width:100%;">
 
Genetic Code
 
Genetic Code
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<div style="padding:5px; margin-top:20px; margin-bottom:10px; background-color:#b3dbce; font-size:30%; font-weight:200; color: #000000; ">
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(Representing and working with the genetic code)
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<div class="keywords">
 
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<b>Keywords:</b>&nbsp;
 
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Representing and working with the genetic code
 
 
</div>
 
</div>
  
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<div style="font-size:118%;">
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== Abstract ==
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<b>Abstract:</b><br />
 
<section begin=abstract />
 
<section begin=abstract />
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<!-- included from "./components/FND-Genetic_code.components.txt", section: "abstract" -->
 
 
The genetic code is conveniently available as a named character vector, via the
 
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,
 
Biostrings package. We access the code, review syntax of how to work with it,
 
and discuss some of its properties.
 
and discuss some of its properties.
 
<section end=abstract />
 
<section end=abstract />
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</div>
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<!-- ============================ -->
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<hr>
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<table>
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== This unit ... ==
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<tr>
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=== Prerequisites ===
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<td style="padding:10px;">
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<!-- included from "./components/FND-Genetic_code.components.txt", section: "prerequisites" -->
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<b>Objectives:</b><br />
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<!-- included from "./data/ABC-unit_components.txt", section: "notes-external_prerequisites" -->
 
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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:
 
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<!-- included from "./data/ABC-unit_prerequisites.txt", section: "biomolecules" -->
 
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*<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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<!-- included from "./data/ABC-unit_prerequisites.txt", section: "central_dogma" -->
 
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*<b>The Central Dogma</b>: Regulation of transcription and translation; protein biosynthesis and degradation; quality control.
 
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<!-- included from "./data/ABC-unit_components.txt", section: "notes-prerequisites" -->
 
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You need to complete the following units before beginning this one:
 
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*[[RPR-Introduction|RPR-Introduction (Introduction to R)]]
 
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{{Vspace}}
 
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=== Objectives ===
 
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<!-- included from "./components/FND-Genetic_code.components.txt", section: "objectives" -->
 
 
This unit will ...
 
This unit will ...
 
* explore the syntax and contents of the named charcater vector that stores the standard genetic code for the Biostrings package;
 
* 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;
 
* note the existence of alternative codes;
 
* introduce an alternative representation as a 3D array.
 
* introduce an alternative representation as a 3D array.
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</td>
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{{Vspace}}
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<td style="padding:10px;">
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<b>Outcomes:</b><br />
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=== Outcomes ===
 
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<!-- included from "./components/FND-Genetic_code.components.txt", section: "outcomes" -->
 
 
After working through this unit you ...
 
After working through this unit you ...
 
* can fetch and use the genetic code from the Biostrings package;
 
* 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.
 
* solve a variety of tasks concerned with the analysis of the code and its display.
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</tr>
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</table>
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<!-- ============================ -->
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=== Deliverables ===
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<hr>
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<!-- included from "./components/FND-Genetic_code.components.txt", section: "deliverables" -->
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<b>Deliverables:</b><br />
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<section begin=deliverables />
 
<!-- included from "./data/ABC-unit_components.txt", section: "deliverables-time_management" -->
 
<!-- included from "./data/ABC-unit_components.txt", section: "deliverables-time_management" -->
 
*<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.
 
*<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.
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<!-- included from "./data/ABC-unit_components.txt", section: "deliverables-insights" -->
 
<!-- included from "./data/ABC-unit_components.txt", section: "deliverables-insights" -->
 
*<b>Insights</b>: If you find something particularly noteworthy about this unit, make a note in your [[ABC-Insights|'''insights!''' page]].
 
*<b>Insights</b>: If you find something particularly noteworthy about this unit, make a note in your [[ABC-Insights|'''insights!''' page]].
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<section end=deliverables />
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<!-- ============================  -->
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<hr>
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<section begin=prerequisites />
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<b>Prerequisites:</b><br />
 +
<!-- included from "./data/ABC-unit_components.txt", section: "notes-external_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:
 +
<!-- included from "./data/ABC-unit_prerequisites.txt", section: "biomolecules" -->
 +
*<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.
 +
<!-- included from "./data/ABC-unit_prerequisites.txt", section: "central_dogma" -->
 +
*<b>The Central Dogma</b>: Regulation of transcription and translation; protein biosynthesis and degradation; quality control.
 +
<!-- included from "./data/ABC-unit_components.txt", section: "notes-prerequisites" -->
 +
This unit builds on material covered in the following prerequisite units:
 +
*[[RPR-Introduction|RPR-Introduction (Introduction to R)]]
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<section end=prerequisites />
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<!-- ============================  -->
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<div id="BIO">
 
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== Contents ==
 
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<!-- included from "./components/FND-Genetic_code.components.txt", section: "contents" -->
 
  
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{{ABC-unit|FND-Genetic_code.R}}
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__TOC__
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== Further reading, links and resources ==
 
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{{#pmid: 8371978}}
 
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{{#pmid: 21819941}}
 
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{{#pmid: 28918301}}
 
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<div class="reference-box">[https://en.wikipedia.org/wiki/Genetic_code '''The Genetic Code''' (Wikipedia)]</div>
 
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<div class="reference-box">[https://www.ncbi.nlm.nih.gov/Taxonomy/taxonomyhome.html/index.cgi?chapter=tgencodes '''Genetic Code Data''' (NCBI)]</div>
 
  
 
{{Vspace}}
 
{{Vspace}}
  
  
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== Notes ==
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== Contents ==
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<!-- included from "./components/FND-Genetic_code.components.txt", section: "notes" -->
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<!-- included from "./components/FND-Genetic_code.components.txt", section: "contents" -->
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<!-- included from "./data/ABC-unit_components.txt", section: "notes" -->
 
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<references />
 
  
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{{ABC-unit|FND-Genetic_code.R}}
  
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<div id="ABC-unit-framework">
 
 
== Self-evaluation ==
 
== Self-evaluation ==
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<!-- included from "./components/FND-Genetic_code.components.txt", section: "self-evaluation" -->
 
 
<!--
 
<!--
 
=== Question 1===
 
=== Question 1===
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-->
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== Notes ==
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{{Vspace}}
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<!-- included from "./components/FND-Genetic_code.components.txt", section: "notes" -->
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<!-- included from "./data/ABC-unit_components.txt", section: "notes" -->
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<references />
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== Further reading, links and resources ==
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{{#pmid: 8371978}}
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{{#pmid: 21819941}}
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{{#pmid: 28918301}}
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<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>
  
 
{{Vspace}}
 
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Revision as of 19:32, 26 January 2018

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:
This unit will ...

  • 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.

Outcomes:
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.

Deliverables:

  • 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.

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:


 



 



 


Contents

Task:

 
  • Open RStudio and load the ABC-units R 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.R and 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.


 

Self-evaluation

Notes

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)

[ PubMed ] [ DOI ]

Santos et al. (2011) The genetic code of the fungal CTG clade. C R Biol 334:607-11. (pmid: 21819941)

[ PubMed ] [ DOI ]

Fimmel & Strüngmann (2018) Mathematical fundamentals for the noise immunity of the genetic code. BioSystems 164:186-198. (pmid: 28918301)

[ PubMed ] [ DOI ]

The Genetic Code (Wikipedia)
Genetic Code Data (NCBI)


 



 

If in doubt, ask! If anything about this learning unit is not clear to you, do not proceed blindly but ask for clarification. Post your question on the course mailing list: others are likely to have similar problems. Or send an email to your instructor.


 

About ...
 
Author:

Boris Steipe <boris.steipe@utoronto.ca>

Created:

2017-08-05

Modified:

2017-09-28

Version:

1.0

Version history:

  • 1.0 First live version
  • 0.1 First stub

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