How can I flip a sequence in IGV (not the strand)?

[dd d]

Dear IGV-Team and to the whole forum,

my problem is the following: At the moment I'm designing primer for the validation of some fusions in cancer genomics. So there's a fusion between two genes, and I want one primer up- and one primer downstream of my fusion. The problem is that sometimes these genes fuse in such a bizarre way that strands are totally messed up. My problem is now that IGV (v. 2.4.8) gives me a sequence for each side of the fusion, but if I want to design primers, that means that I need the sequence "the other way around":

As an example:

Gene 1: TAGTCGTTG |(breaking point 1)

Gene 2: TGGCGATCT |(breaking point 2)

The region navigator now gives me these two sequences. Of course if the fusion is on the minus-strand I'm switching the strand.

But the fused gene which I want to validate via PCR/ Sanger looks like this: TAGTCGTTG || TCTAGCGGT

So my problem is that I don't find a way to get the sequence of the second gene "flipped around". IGV gives me "TGGCGATCT" but what I need is "TCTAGCGGT".

Does anybody has an advice for me?

Many thanks in advance,

David

[Michael Bunnemeyer]

It should be simple to write an utility for IGV tools to reverse a sequence.

Michael

--

---
You received this message because you are subscribed to the Google Groups "igv-help" group.
To unsubscribe from this group and stop receiving emails from it, send an email to igv-help+u...@googlegroups.com.
To view this discussion on the web visit https://groups.google.com/d/msgid/igv-help/fa75ad6a-e1eb-4e58-bc9e-aaae897d4ef4%40googlegroups.com.
For more options, visit https://groups.google.com/d/optout.