Question: tests for negative selection
1
gravatar for evo_genomics
4.9 years ago by
evo_genomics40
Pakistan
evo_genomics40 wrote:

I estimated the synonymous and non synonymous (ka/ks) ratio of a gene and got negative selection in human.  Now what kind of tests I can apply further ?

selection negative gene • 2.0k views
ADD COMMENTlink modified 4.9 years ago by Siva1.6k • written 4.9 years ago by evo_genomics40
0
gravatar for Brice Sarver
4.9 years ago by
Brice Sarver3.0k
United States
Brice Sarver3.0k wrote:

Site frequency spectrum analyses for deviations from neutrality: Tajima's D, Fu and Li's F, Fu and Li's D2, etc.

Nucleotide composition, codon bias (if coding).

Choose among selective models using codeml in PAML.

REL/FEL/IFEL/SLAC implemented in HyPhy. FUBAR. Shifts in biochemical properties. The DataMonkey web server will perform these analyses.

Your question is extremely open ended, and it is often the case that you don't want to do analyses "just because." It's more about answering what is important for your system than throwing everything at the wall and seeing what sticks, so to speak. I hope these suggestions will give you some ideas.

ADD COMMENTlink written 4.9 years ago by Brice Sarver3.0k
0
gravatar for evo_genomics
4.9 years ago by
evo_genomics40
Pakistan
evo_genomics40 wrote:

thanks.

I  m checking the selection in gene and expecting it is positively evolving. I have applied codon substitution models to estimate ka/ks using different tools. I wanted to know, what kind of selection force is acting on gene in human lineage. Results of ks/ks shows that gene is under negative selection. I suppose, might be there are few positively evolving sites as compare to sites that are under negative selection in gene. Then I applied Tajima's D and Fu and Li test to check weather it deviates from neutrality in population or not. I didn't got significant results for positive selection.

I have review different  research papers. they go towards structural side after finding negative selection on a gene.

I am interested in knowing, from evolutionary aspect what are the possible ways for me to the proceed study.

 

ADD COMMENTlink written 4.9 years ago by evo_genomics40
0
gravatar for Siva
4.9 years ago by
Siva1.6k
United States
Siva1.6k wrote:

If you are suspecting only few sites in the human gene are under positive selection, a likelihood-ratio test (LRT) using branch-site model in codeml might be an appropriate test and also to find those sites. I found this tutorial very useful for the LRT.

ADD COMMENTlink written 4.9 years ago by Siva1.6k
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