3 replies to this topic

[tiggeria]

I just started using Primer-BLAST at NCBI, but I could not get rid of the same base runs in a row.  e.g., I could not limit the primers with ".....GGGG".

In the normal Primer3, there is this option "Max Poly-X:", but I could not see it in Primer-BLAST. Does anybody know if this option is hidden somewhere in Primer-Blast?

When we are at it, does Primer-Blast have the "Max 3' Stability" option in normal Primer3?

Edited by tiggeria, 21 October 2009 - 10:23 AM.

[Mighty Mouse]

tiggeria, on Oct 21 2009, 01:31 PM, said:

I just started using Primer-BLAST at NCBI, but I could not get rid of the same base runs in a row.  e.g., I could not limit the primers with ".....GGGG".

In the normal Primer3, there is this option "Max Poly-X:", but I could not see it in Primer-BLAST. Does anybody know if this option is hidden somewhere in Primer-Blast?

When we are at it, does Primer-Blast have the "Max 3' Stability" option in normal Primer3?

I've used Primer-BLAST...I don't know that PrimerBLAST has a Max Poly-X option; but if you go to the bottom of the page and click "advanced paramaters" there is a Max 3' end complementarity option you can use for the Max 3' stability. Overall I have to say I'm pretty disappointed in PrimerBLAST. The output is not ranked in any way that I can tell, thus making it very difficult to choose which primer set to try. And clearly they don't recapitulate all the options in Primer3 even though they make use of that platform.

MM

[tiggeria]

Thanks, MM for your suggestions.

Unfortunately, it does not help much. I still see 5 A's and 5 G's come up in the primers in other part of the primers. So now my conclusion is Primer-Blast is useless for qrt-pcr primer design. These primers are just an eye sore.

Just for record. To anybody who will be reading this post, I have emailed NBCI Informtion Technolgy help, and the official answer is NO. There is no "Max-Poly-X" setting in Primer-Blast. I am having trouble understanding why they would put any effort to develope this Primer-Blast thing at all.

[tiggeria]

An update on this.

Good news: the folks at NCBI have put the "Max-Poly-X" option in the Primer-Blast. It is in the "Advnaced Parameters".  Maybe my inquiry triggered this, who knows. Kudos to whoever did it!

Now, it will make my primer design fast and easy.

Edited by tiggeria, 09 November 2009 - 11:19 AM.