5 replies to this topic

[Lotus Japonicus]

I'm having trouble with primer design and was wondering if there's an alternative out there to netprimer. I can't access net primer at the moment, I presume it's down. I've found OligoAnalyzer but I'm not too sure about the interface so was wondering if there were any more tools out there for comparing primers and, also, if anyone knows what's wrong with netprimer and when it will be back up.

Thanks

[jiajia1987]

you can try primer3.0.

[Lotus Japonicus]

jiajia1987, on Jun 24 2009, 04:33 AM, said:

you can try primer3.0.

Does primer 3 allow you to do alignments and such to look for regions where the primers are likely to dimerise with themselves and each other. I use primer3 to design primers but haven't ever noticed that. Will take a look now.

[microgirl]

IDT (idtnda.com) has a really good primer design tool. It has all sorts of advanced features that I never use - LOL.

[Trof]

Lotus Japonicus, on Jun 24 2009, 11:35 AM, said:

jiajia1987, on Jun 24 2009, 04:33 AM, said:

you can try primer3.0.

Does primer 3 allow you to do alignments and such to look for regions where the primers are likely to dimerise with themselves and each other. I use primer3 to design primers but haven't ever noticed that. Will take a look now.

Primers 3 makes score for primers making dimers in general (any column in the results) or at 3' end (3' column). Both for each separate primer and for primer pair.  Look for these scores, or set lower limits to design primers that dimerase less.

Personaly I use maximum 6 for any, and 3 for 3' and choose those pairs that have lower values.

[wilson_trace]

Lotus Japonicus, on Jun 23 2009, 08:43 AM, said:

I'm having trouble with primer design and was wondering if there's an alternative out there to netprimer. I can't access net primer at the moment, I presume it's down. I've found OligoAnalyzer but I'm not too sure about the interface so was wondering if there were any more tools out there for comparing primers and, also, if anyone knows what's wrong with netprimer and when it will be back up.

Thanks

Hi

I have been using NetPrimer for analyzing primers. Its working well.
Here is the link - http://www.premierbi...imer/index.html

Cheers