Difference between revisions of "CS382:Unit-phylogeny"
(New page: Assembling a phylogenetic tree - Look at models available from the bioinformatics toolbench and experiment with different ways comparing protein similarity. This could be tied into a lect...) |
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| + | == Basis == | ||
| + | phylogenetic trees are structures which show the homology between similar proteins, in different organisms. They | ||
| + | |||
Assembling a phylogenetic tree - Look at models available from the bioinformatics toolbench and experiment with different ways comparing protein similarity. This could be tied into a lecture on protein folding as protein homology like indicative of phylogeny. | Assembling a phylogenetic tree - Look at models available from the bioinformatics toolbench and experiment with different ways comparing protein similarity. This could be tied into a lecture on protein folding as protein homology like indicative of phylogeny. | ||
Cladistics (constructing a phylogenetic tree). Start with a common protein or gene amongst a group of organisms and construct a model for how they diverged evolutionarily based on evidence from that gene. This could also start simpler with looking at homologies and analogies and constructing a tree based on that (old way), then moving to the more cutting research with the genes. Would give an opportunity to talk about the computing power behind searching large databases of proteins or nucleotides. | Cladistics (constructing a phylogenetic tree). Start with a common protein or gene amongst a group of organisms and construct a model for how they diverged evolutionarily based on evidence from that gene. This could also start simpler with looking at homologies and analogies and constructing a tree based on that (old way), then moving to the more cutting research with the genes. Would give an opportunity to talk about the computing power behind searching large databases of proteins or nucleotides. | ||
| + | |||
| + | == Comments == | ||
| + | Pros | ||
| + | |||
| + | Cons | ||
| + | * A lot of the software used to do this is largely inaccessible. | ||
| + | |||
| + | Comments | ||
| + | * Taking a bunch of trees and then merging them into a single tree that simultaneously let you see how close something is in respect to multiple variables is particularly computationally expensive. | ||
| + | * Potentially make a friendly GUI to mpiblast and MrBayes or something similar. | ||
| + | |||
| + | == To Do == | ||
| + | * Currently looking at Biology Workbench or other software for construction. | ||
| + | * Look at if there's a way to use mpiblast results to generate a tree. | ||
Latest revision as of 10:41, 28 January 2009
Basis
phylogenetic trees are structures which show the homology between similar proteins, in different organisms. They
Assembling a phylogenetic tree - Look at models available from the bioinformatics toolbench and experiment with different ways comparing protein similarity. This could be tied into a lecture on protein folding as protein homology like indicative of phylogeny.
Cladistics (constructing a phylogenetic tree). Start with a common protein or gene amongst a group of organisms and construct a model for how they diverged evolutionarily based on evidence from that gene. This could also start simpler with looking at homologies and analogies and constructing a tree based on that (old way), then moving to the more cutting research with the genes. Would give an opportunity to talk about the computing power behind searching large databases of proteins or nucleotides.
Comments
Pros
Cons
- A lot of the software used to do this is largely inaccessible.
Comments
- Taking a bunch of trees and then merging them into a single tree that simultaneously let you see how close something is in respect to multiple variables is particularly computationally expensive.
- Potentially make a friendly GUI to mpiblast and MrBayes or something similar.
To Do
- Currently looking at Biology Workbench or other software for construction.
- Look at if there's a way to use mpiblast results to generate a tree.
