I'm looking for a tool to compare two fungal proteomes. The proteome set consists of around 11,000 different proteins each that were predicted in-silico from two sequencing experiments. One is from a parent fungal strain, the second proteome is that of the parent strain after passage in culture. There are phenotypic changes in the organism after passage, so I'd like to know which of the proteins between the two sets are different from one another. I've done a protein blast but it is still a big task to go through the blast output to see which proteins don't have 100% identity and coverage.
Is there a tool that could make me do this quicker?
Many thanks in advance