Question: visualize amino acid changes in genes that are positively selected after codeml run
0
gravatar for Mehmet
5 months ago by
Mehmet470
Japan
Mehmet470 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 • 172 views
ADD COMMENTlink modified 5 months ago by h.mon27k • written 5 months ago by Mehmet470
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 5 months ago by jrj.healey13k
0
gravatar for h.mon
5 months ago by
h.mon27k
Brazil
h.mon27k 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 5 months ago • written 5 months ago by h.mon27k

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 5 months ago by Mehmet470
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