Difference between revisions of "BIN-ALI-Dotplot"
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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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Dotplot | Dotplot | ||
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| − | + | (Computation and interpretation of dotplots) | |
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| + | <b>Abstract:</b><br /> | ||
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| + | <b>Deliverables:</b><br /> | ||
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| + | <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 /> | ||
| + | This unit builds on material covered in the following prerequisite units:<br /> | ||
| + | *[[BIN-ALI-Similarity|BIN-ALI-Similarity (Measuring Sequence Similarity)]] | ||
| + | <section end=prerequisites /> | ||
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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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| + | === DotPlots and the Mutation Data Matrix === | ||
| + | Before we start calculating alignments, we should get a better sense of the underlying sequence similarity. A Dotplot is a perfect tool for that, because it displays alignment-free similarity information. (For a deeper introduction into dotplots, see the [[BIN-ALI-Dotplot|Dotplots learning unit]]). Let's make a dotplot that uses the BLOSUM62 Mutation Data Matrix to measure pairwise amino acid similarity. The NCBI makes its alignment matrices available by ftp. They are located at ftp://ftp.ncbi.nih.gov/blast/matrices - for example here is a link to the [ftp://ftp.ncbi.nih.gov/blast/matrices/BLOSUM62 '''BLOSUM62 matrix''']<ref>That directory also contains sourcecode to generate the PAM matrices. This may be of interest if you ever want to produce scoring matrices from your own datasets.</ref>. | ||
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== Self-evaluation == | == Self-evaluation == | ||
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=== Question 1=== | === Question 1=== | ||
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| + | == Further reading, links and resources == | ||
| + | <!-- {{#pmid: 19957275}} --> | ||
| + | <!-- {{WWW|WWW_GMOD}} --> | ||
| + | <!-- <div class="reference-box">[http://www.ncbi.nlm.nih.gov]</div> --> | ||
| + | == Notes == | ||
| + | <references /> | ||
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*0.1 First stub | *0.1 First stub | ||
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Latest revision as of 09:26, 25 September 2020
Dotplot
(Computation and interpretation of dotplots)
Abstract:
...
|
Objectives: |
Outcomes: |
Deliverables:
Prerequisites:
This unit builds on material covered in the following prerequisite units:
Sorry!
This page is only a stub; it is here as a placeholder to establish the logical framework of the site but there is no significant content as yet. Do not work with this material until it is updated to "live" status.
Evaluation
Evaluation: NA
This unit is not evaluated for course marks.
Contents
Task:
- Read the introductory notes on Dotplots for sequence comparison.
Self-evaluation
Further reading, links and resources
Notes
About ...
Author:
- Boris Steipe <boris.steipe@utoronto.ca>
Created:
- 2017-08-05
Modified:
- 2017-08-05
Version:
- 0.1
Version history:
- 0.1 First stub
This copyrighted material is licensed under a Creative Commons Attribution 4.0 International License. Follow the link to learn more.
Sorry!
This page is only a stub; it is here as a placeholder to establish the logical framework of the site but there is no significant content as yet. Do not work with this material until it is updated to "live" status.
