Degenerate primers desing software

[rexxi]

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

[Phoenix_ICE]

dCAPS

http://helix.wustl.edu/dcaps/dcaps.html

Genefisher2

http://bibiserv.techfak.uni-bielefeld.de/genefisher2/

[maubp]

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.

[SES]

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.