Hi I am trying to get deep into some definitions in bioinformatics. Now I'm counting the paralogs in a viral genome. I found this page. What I did is that I did a blast search of those viral orfs against themselves. (blastp -query viralorfs -db viralorfs). So I need a specification regarding my results.
After blast I got:
1)gene1 - gene1 100% sim
2)gene1 - gene61 88% sim
3)gene2 - gene2 100% sim
4)gene2 - gene5 60% sim
5)gene2 - gene11 78% sim
6)gene3 - gene3 100% sim
7)gene3 - gene37 45% sim
8)gene3 - gene34 38% sim
I excluded from my final results of 100% similarity between the same genes, but in some cases, I had more than 2 hits
2)gene1 - gene61 88% sim
4)gene2 - gene5 60% sim
5)gene2 - gene11 78%sim
7)gene3 - gene37 45% sim
8)gene3 - gene34 38% sim
My question is: In this case, the number of paralogs is 3 or 5? Thank you in advance
