homozygous primer for PCR
Hi all,
To design the primer for MiSeq, I found that it might be hard to design a perfect primer for those homozygous region.
say, for a 22 bp primer, if I use blast program to seek its homo condition, I found 17 bp could be matched in other chrom, some of this 5 bp are in the 5' of the primers, while others are randomly distributed.
So is there any guidance (ref?) for this development?
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Why exactly are you trying to design primers for a MiSeq? Are you instead trying to design PCR primers to amplify a genomic region that you then want to sequence (presumably looking for look frequency changes, since otherwise a MiSeq is overkill)?