BIN-SEQA-Composition

Analysis of Sequence Composition

(Analysis of sequence composition.)

 

Abstract:

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

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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.

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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.

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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.

This unit builds on material covered in the following prerequisite units:

• BIN-SEQA-Concepts (Concepts of Sequence Analysis)

 

This page is tagged for revision; expect changes and proceed with caution.

 

 

Contents

Task:

• Read the introductory notes on "Composition" as a paradigm for sequence analysis.

EMBOSS Tools

 

Task:

• Navigate to an instance of the "EMBOSS explorer" e.g. at bioinformatics.nl

Local composition

1. Find pepinfo under the PROTEIN COMPOSITION heading.
2. Retrieve the MYSPE Mbp1 related sequence from your R database, e.g. with something like
   cat(db$protein[db$protein$name == "UMAG_1122"), "sequence"]
3. Copy and paste the sequence into the input field.
4. Run with default parameters.
5. Scroll to the figures all the way at the bottom.
6. Do the same in a separate window for yeast Mbp1.
7. Try to compare ... (kind of hard without reference, overlay and expectation, isn't it?)

 

Global composition

1. Find pepstats under the PROTEIN COMPOSITION heading.
2. Paste the MYSPE Mbp1 sequence into the input field.
3. Run with default parameters.
4. Do the same in a separate window for yeast Mbp1.
5. 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.
• 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.

 

 

Self-evaluation

Notes

Further reading, links and resources

 

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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.

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About ...
 
Author:

Boris Steipe <boris.steipe@utoronto.ca>

Created:

2017-08-05

Modified:

2017-11-14

Version:

1.0

Version history:

• 1.0 First live
• 0.1 First stub

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