Question: visualize amino acid changes in genes that are positively selected after codeml run
0
gravatar for Mehmet
12 months ago by
Mehmet510
Japan
Mehmet510 wrote:

Dear All,

can anyone suggest a tool/software to visualize amino acid changes of positively selected genes? I have run codeml and detected positively selected genes, and now I want to produce 3D graphs of genes by emphasizing amino acid changes.

Do you know any tool or software for this?

alignment genome gene • 295 views
ADD COMMENTlink modified 12 months ago by h.mon29k • written 12 months ago by Mehmet510
1

This is not specifically what you asked for, but you can create an attributes file, and render the 3D structure of the protein by selection in UCSF Chimera, if you have a 3D structure for that protein.

(see https://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/defineattrib/defineattrib.html )

ADD REPLYlink written 12 months ago by Joe16k
0
gravatar for h.mon
12 months ago by
h.mon29k
Brazil
h.mon29k wrote:

The ETE3 toolkit wraps codeml and, in addition to performing selection tests, it produces some nice figures. It also has an interactive GUI mode where one can customize / explore the analyses and graphics. For examples, see:

http://etetoolkit.org/documentation/ete-evol/

http://etetoolkit.org/docs/latest/tutorial/tutorial_adaptation.html

http://etetoolkit.org/cookbook/ete_evol_codeml_configuration_files.ipynb

I am not sure what you mean by "3D graphs of genes by emphasizing amino acid changes", though. Are you talking about protein structure?

ADD COMMENTlink modified 12 months ago • written 12 months ago by h.mon29k

Thank you for your suggestions. I mean I want to show where amino acid changes of a protein occurred due to positive selection.

ADD REPLYlink written 12 months ago by Mehmet510
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