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Old 08-20-2012, 01:20 PM   #1
rexxi
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Question Degenerate primers desing software

Hi all of you,

I'm looking for a software to design degenerate primers to make a multiplex PCR to try to close a little genome who has 10 contigs. I tried to use some primers developers softwares but these couldn't give me what I want. Do somebody know a tool that could help me?

thanks a lot
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Old 08-20-2012, 04:11 PM   #2
Phoenix_ICE
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dCAPS
http://helix.wustl.edu/dcaps/dcaps.html

Genefisher2
http://bibiserv.techfak.uni-bielefeld.de/genefisher2/
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Old 08-21-2012, 12:48 AM   #3
maubp
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If you only have 10 gaps to close, and can guess the placement of some of them using a reference related species, then specific primers should be fine. I appreciate if you don't know which order the contigs run in, this could be harder.

I would consider a mixed primer strategy - design up to 20 specific primers (both ends of each fragment) and do a mixed PCR (with multiple primers together) then size selection of any products. Talk to your lab colleagues about this.

Last edited by maubp; 08-22-2012 at 07:33 AM. Reason: typo
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Old 08-22-2012, 07:17 AM   #4
SES
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Quote:
Originally Posted by rexxi View Post
Hi all of you,

I'm looking for a software to design degenerate primers to make a multiplex PCR to try to close a little genome who has 10 contigs. I tried to use some primers developers softwares but these couldn't give me what I want. Do somebody know a tool that could help me?

thanks a lot
Can you estimate the size of the gaps based on the genome size? In doing this type of work in the past, I found it really helps to know the expected gap size when optimizing PCR reactions. For example, if you expect a gap to be around 4kb, you would use a different set of conditions than if you expected a gap of 100 bp.
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