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A real world phylogenetic analysis
Objectives
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Futher Practice
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Objectives
Have some fun and explore with the tools we have already used.
Given the following Accessions:
- AF197588.1
- AF197589.1
- AF197590.1
- AF197591.1
- AF197592.1
- AF197593.1
- AF197594.1
- AF197595.1
- AF197596.1
- AF197597.1
- AF197598.1
- AF197599.1
Take some time to consider the following:
- Learn what purpose these genes have.
- What organisms are they from?
- Are these organisms closely related?
- Is the universal genetic code appropriate?
- In what context have these sequences been studied?
Perform the following analyses:
- Align them and examine your alignment for problems.
- Find the paper(s) which use these sequences and look at the tree(s) they generated.
- Generate your own tree using just these taxa. (This will take a while)
If we can, I think it would be fun to do the following while waiting for trees to calculate:
- Create an hmm from your alignment
- Start a search in genbank/nr for similar sequences using your hmm
Homework
For homework, record your analyses and make some inferences regarding
the solvability of the problem which these sequences seek to solve.
Create phylogenetic trees for these sequences using two optimality
criteria and bootstrap the results.
Created: Wed Sep 15 00:58:22 EDT 2004 by Charles F. Delwiche
Last modified: Mon Nov 8 15:49:44 EST 2004
by Ashton Trey Belew.
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