I've two sets of protein sequences for a particular organism for which the genome sequence is available to us.
One of the protein sets is derived from comparing the genome with all the proteins of a related organism using a protein-genome alignment program.
The second protein set was derived from a translated cDNA library from the same organism.
I wish to find out the equivalent pair of proteins(supposedly almost identical) from these two sets.
Can anybody suggest any good method for this? Can I use 'reciprocal blast best hits' method?
Thanks in advance