Expected Preparations:

  Biomolecules:
The molecules of life; The genetic code; Nucleic acids; Amino acids; Protein folding; Post-translational modifications and protein biochemistry; Membrane proteins; Biological function.
   [BIN-SEQA]
Concepts 		 
  If you are not already familiar with the prior knowledge listed above, you need to prepare yourself from other information sources.   The units listed above are part of this course and contain important preparatory material.  
Keywords: Analysis of sequence composition.
Objectives:

This unit will …

  • … introduce basic compositional amino acid analysis;

  • … teach how to prodcue barplots of enrichment ratios;

 Outcomes:

After working through this unit you …

  • … are familar with comparing observed to reference frequencies;

  • … can use tools from the seqinr package for simple amino acid analysis;

  • … can produce barplots of log(ratio) data.

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.

Evaluation:

NA: This unit is not evaluated for course marks.

Contents

The most basic step of sequence analysis is to ask: what amino acids does a sequence contain.

Task…

EMBOSS Tools

 

Task…

Local composition 1. Find pepinfo under the PROTEIN COMPOSITION heading. 1. Retrieve the MYSPE Mbp1 related sequence from your R database, e.g. with something like
cat(myDB\(protein[myDB\)protein$name == “PHD1_SACCE” , “sequence”]) 1. Copy and paste the sequence into the input field. 1. Run with default parameters. 1. Scroll to the figures all the way at the bottom. 1. Do the same in a separate window for yeast Mbp1. 1. Try to compare … (kind of hard without reference, overlay and expectation, isn’t it?)

 

Global composition 1. Find pepstats under the PROTEIN COMPOSITION heading. 1. Paste the MYSPE Mbp1 sequence into the input field. 1. Run with default parameters. 1. Do the same in a separate window for yeast Mbp1. 1. Try to compare … are there significant and unexpected differences?

 

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. This ensures that your data and code remain up to date when we update, or fix bugs.
  • Type init() if requested.
  • Open the file BIN-SEQA-Composition.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.

 

Questions, comments

If in doubt, ask! If anything about this contents is not clear to you, do not proceed but ask for clarification. If you have ideas about how to make this material better, let’s hear them. We are aiming to compile a list of FAQs for all learning units, and your contributions will count towards your participation marks.

Improve this page! If you have questions or comments, please post them on the Quercus Discussion board with a subject line that includes the name of the unit.

References

Page ID: BIN-SEQA-Composition

Author:
Boris Steipe ( <boris.steipe@utoronto.ca> )
Created:
2017-08-05
Last modified:
2022-09-14
Version:
1.1
Version History:
–  1.1 2020 Maintenance
–  1.0 First live
–  0.1 First stub
Tagged with:
–  Unit
–  Live
–  Has lecture slides
–  Links to R course project

 

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