I want to compare protein (amino acid) sequences of two organisms on a genome scale. That is, if I have organism A with 10 proteins (hypothetical) and another organism B with 10 proteins I would like to see what proteins in B are orthologues to A based on sequence identity/similarity. Theoretically where I can tabulate the results as follows.
Protein from A | Protein from B and Identity to A
1 | 4 80%
2 | 1 45%
3 | 10 30%
4 | --- No orthologue
5 | 9 65%
I guess my question is what tools are out there to do this on a large scale not just one by one through NCBI blast.