I have done blast with Affymetrix probe sets of the HG-U133 Plus 2 with NCBI human refSeq database. So I would like to know what will be the length of cross-hybridization of probes with RefSeq database. I mean that the number of base pairs.
For example, when we consider for 50 mer probes, if the probes are matching with database sequences greater then or equal to 25 base pair then we usually consider this is a cross-hybridization. For 25 mer probes, I can consider >=17bp length as the cross hybridization. Help me out to solve this problem.
Thanks in Advanced.
With regards, Nelson