Hello, I am new in field of bioinformatics. I have to do similarity search on protein sequences but the number of bacterial strain is large. There are various tools available for genome comparison but I don't know any tool that compare entire proteome of several bacterial strains. BLAST is used for similarity search tool but I don't have an idea of maximum number of bacterial strains that can be used for one Blast Search. Does anyone know of a tool that will help me to identify conserved regions in 5500 bacterial strains.