Bioinformatics Week 7

Selection analysis: Tries to identify whether natural selection is occurring or not as well as if the selection is to get rid of a certain sequence or promote a sequence. Then how this selection affects the species. 
3 types of selection

• Negative: Removes a detrimental mutation. 
• Positive: Bennificial mutation promoted. 
• Balancing/Diversfying seleciton: Favors the maintenance of multiple variations of a sequence in a diverse environment. 

When measuring selection there are two standard techniques

• Tajima's D: Based on a few standard principles. The genetic regions near a region which is being selected for get dragged into the selection process (genetic hitchhiking). The length of the genetic region is dependent on the rate of recombination. Theta equals to Pi when no selection is occurring. When theta is greater than Pi then positive selection is occurring. When theta is less than Pi then balancing selection is occurring. Advantages: Good however can be fooled by other factors (ex:bottleneck mistaken for positive selection). Therefore after you preform Tajima's D you must preform other tests to single out chances of error in your data. 
• dN/dS: This calculates the ratio of nonsynonmous mutations (change the protein) to synonemous mutations (doesn't affect protein). Very good for figuring out if there are specific sites which are being selected for and then figure out which codons are being selected for. No selection dN/dS=1, negative selection dN/dS<1, positive selection dN/dS>1. 

There are two popular ways of quantifying selection (measuring variation)

• Theta: Based on the number of variable(changed between species) sites in a sample 
• Pi: Based on the average number of differences between sequences. More sensitive to the frequency of a variation.