BlastN - Optimal recipocal blast command line options ?

Question

[sunnykevin97]

Hi

Please do let me know some suggestions, optimal parameters for performing reciprocal blastN ? The blast output I'll be using as a reference set for finding orthologs by performing pariwise blast.

Thanks kevin

Answer 1

[lieven.sterck]

well, for one you are better of running blast for orthology detection on protein level, thus using blastP in stead of blastN.

otherwise there are not really optimal parameters, the default should do in most cases. The thing with reciprocal blast analyses is that you have similar top hits, so as long as you run blast A-B in the same setting as B-A you should be fine.