Bioinformatics software have been used in the analysis of sequences protein CD59 of stem cells. Using these algorithm in combination with protein CD59 and immune information algorithms lead to better prediction of the destiny of transplant stem cells. This knowledge may help improve the efficacy and safety of stem cells used in transplantation. CD59 protein on cell surface of stem cells isolation from Adipose tissue for Orthologs in other species (human, chimpanzee, monkey ,baboon ,pig ,rabbit,

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... rat) play an important role on rejection or binding with the complement of the immune system .In this search ,we find many strong epitopes by software bioinformatics in MHC class I HLA-A02-01, MHC class II HLA-DR B 1010 receptor with CD59 donor .these data may help to design new peptide with active site binding to immune system complement receptor from CD59 donor after isolation from adipose tissue .