設計SNP的primer

Question

rs10835210: Neighbor SNPs contain DIP type SNP and cover each other. To ignore these SNPs, check "Exclusive DIP type SNPs" option

不太了解裡面的DIP type SNP是什麼意思

另外

insert /deletion SNP 是什麼意思啊?

查了字典也不太了解這兩個詞搭上SNP後是要表達什麼

Update:

我是在這邊看到的 http://genepipe.ngc.sinica.edu.tw/seqtool/pages/ge...

這是一種幫忙設計primer的格式

不過是專用在那系統上而已

Answer 1

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hm, can you tell me where you see the message? I think I know what it is talking about, but not completely sure.

2008-10-14 00:22:01 補充：

Ok, so here's what I think:

The program you're referring to access dbSNP for SNP information. But dbSNP doesn't just catalog SNPs, it contains all kinds of simple genetic polymorphisms, which includes INDELs or DIPs. INDELs and DIPs are essentially the same, (INDEL is INsertion/DELetion, DIP is Deletion Insertion Polymorphism). These are just short nucleotides insertion and deletions relative to a reference genome. They are not "SNP" per se, but because they are found in dbSNP, the author of the program just called them "DIP type SNP". SNPs should really be just single base pair substitutions.

So in the case of rs10835210, I think the program is telling you that in addition to the substitution itself, there's a nearby (or perhaps the same position) INDEL that would in some cases even delete or duplicate the SNP position, so gives you trouble making a primer. The system appears to be unable to cope with this anyhow, since you don't seem to be able to download a sequence if you don't choose to ignore the "DIP type SNPs".

As for insert /deletion SNPs, it's the same logic. They are not really SNPs, but insertion/deletions are reported in dbSNP, so someone added the term "SNP" to them.

Technically, if you talk about "SNPs", it is implied to be single base pair substitution polymorphisms. If you want to specify insertion/deletions, you need to say INDEL, and don't confuse people by adding SNP after that.

Does this make sense?

Source(s): I'm a graduate student in Genetics