Calculating E-value from Exonerate and choosing minimum percentage identity.

Question

[8d8fc19e]

I have aligned genes in one species to genes in another and would like to find out how many genes of the query are presents in the target.

To do this, I have used Exonerate. I am able to output the percentage identity using Exonerate. However, to have a more robust measure of whether genes correspond to one another in each species, I would like to E-values. Is there a way to output these in Exonerate?

I am also unsure of where to set my threshold for percentage identity. I know both of these species had a common ancestor if that is any help?

Answer 1

[Jean-Karim Heriche]

As far as I remember (it's been a while since I used it) exonerate doesn't produce e-values. You could use the alignment scores if you need something else than the % identity. Check the options available to the roll-your-own format (--ryo option) to see what can be output by the program.