Difference between revisions of "BIN-ALI-Dotplot"
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You need to complete the following units before beginning this one: | You need to complete the following units before beginning this one: | ||
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*Read the introductory notes on {{ABC-PDF|BIN-ALI-Dotplot|Dotplots for sequence comparison}}. | *Read the introductory notes on {{ABC-PDF|BIN-ALI-Dotplot|Dotplots for sequence comparison}}. | ||
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| + | === DotPlots and the Mutation Data Matrix === | ||
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| + | 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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Revision as of 03:37, 23 October 2017
Dotplot
Keywords: Computation and interpretation of dotplots
Contents
This unit is under development. There is some contents here but it is incomplete and/or may change significantly: links may lead to nowhere, the contents is likely going to be rearranged, and objectives, deliverables etc. may be incomplete or missing. Do not work with this material until it is updated to "live" status.
Abstract
...
This unit ...
Prerequisites
You need to complete the following units before beginning this one:
Objectives
...
Outcomes
...
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
Evaluation: NA
- This unit is not evaluated for course marks.
Contents
Task:
- Read the introductory notes on Dotplots for sequence comparison.
Further reading, links and resources
Notes
Self-evaluation
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:
- 2017-08-05
Version:
- 0.1
Version history:
- 0.1 First stub
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