Hello there,
I have to detect orthologs by using reciprocal BLAST, i.e. blasting the set A against the set B and then blasting the set B against the set A.
If the sets A and B contain redundant entries, how should I deal with the redundancies in both sets (query sets and subject sets)? I was thinking about grouping the genes with the top scores into one. Someone told me that grouping them by scores won’t work since it depends on the sequence length. Another idea was to make the non-redundant sets for A and B, which contains the representatives from a cluster of similar sequences within each set. I don’t want to go down this road since taking a representatives means a loss of information.
Can you give me an advice on this? If there is any other thing that I should watch out for when doing the reciprocal blast, please let me know. I’d appreciate it very much.