Does anyone happen to know of any software/ online tool which allows me to do the following:
I would like to align several protein sequences (over 100) from one organism with a similar number from a different organism, to find which protein(s) from organism X are most like those from organism Y, or even which domains. I am already aware of the many MSA tools available online, but none of them exclude intra-species homology (I am only interested in where similarities occur between the two organisms). Checking protein by protein is obviously doable but would require an exhaustible number of alignments to be made. Ideally I would give this tool all of the protein sequences (FASTA) from one organism, and 1 sequence from the second organism, and it would return to me a list of proteins with the highest scoring homology, and where in the sequence the similarities occur. Alternatively I would give it all from both organisms and it would do a similar, although I appreciate this is far less likely to work.
Any suggestions would be greatly appreciated,