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Protegen: Frequently Asked Questions

1. For the options of “No similarity to Human Proteins” and “No similarity to Mouse Proteins” in Protegen Query, what is the cutoff for this similarity field? What genome version of humans and mouse were used?

The E-value cutoff for this BLAST similarity field is 10-6, which is the same E-value cutoff used in the Vaxign program The human protein sequences were retrieved on Feb 26, 2008, from ftp://ftp.ncbi.nih.gov/refseq/H_sapiens/mRNA_Prot/human.protein.faa.gz. The mouse protein sequences were retrieved on March 5, 2008 from ftp://ftp.ncbi.nih.gov/refseq/M_musculus/mRNA_Prot/mouse.protein.faa.gz.