primer design

[razibus]

I'm using Oligo 7 for designing primer but one of the weakness of this software is that you have to check for possible SNPs in the primers you get.

I'm trying to see if there is a better software and I made a list of other softwares :
- Primer Premier
- NoePrimer
- Primer Express 3.0
- Vector NTI

Do you know other software or maybe webtools like Primer3?

Which one are you using and why do you think it's the best one?

[krobison]

If you of a programming bent, Primer3 has the advantage you can control just about everything via options & fit it into a pipeline.

[biznatch]

Primer-BLAST has the option to avoid regions with SNPs, look under the Advanced Parameters section.

[cascoamarillo]

I really like Oligo Explorer from Gene Link:

http://www.genelink.com/tools/gl-oe.asp

[razibus]

Primer-BLAST is quite nice but it is also slow and you cannot do batch requests.

I tested Primer Z and RExPrimer which are good webtools but not as flexible as Primer-BLAST.

Oligo Explorer looks nice but does it take into account SNPs?

Anyway all these tools are not bad but I'm trying to find something more NGS oriented. When you get mutations from your sequencing you could get a lot of mutations to check on more DNA samples. I would like to find a tool which uses genomic position where you get your mutation for example, a little like Halo genomics does with their design wizard.

[chriscelone]

Does anyone have any experience with primer design of oncogenes utilizing Sequenom software?

[folli]

It might not directly answer your question regarding SNPs, but for straightforward primer design cases give GeneWarrior a try. It's based on Primer3 but you can interactively select your targets and exclusions by drag and drop.

The step-by-step tutorial is here: http://genewarrior.com/docs/tut_primerdesign.jsp