Results are different from https://www.bioinformatics.nl

primer3-org / primer3plus

Primer3Plus is an advanced web interface for primer3.

GNU General Public License v3.0

29 stars 12 forks source link

Results are different from https://www.bioinformatics.nl #16

Closed FredericBGA closed 2 years ago

FredericBGA commented 2 years ago

Hello,

I've installed a Primer3plus website from this git repository. But when, for example, I run the "Check Primer" task the results (and the interface also) are quite different.

Sequence: aatcatcatacgac

Using www.bioinformatics.nl
Length: | 14 bp
Tm: | 32.0 °C
GC: | 35.7 %
ANY: | 4.0
SELF: | 2.0
3' Stability: | 7.8 ΔG

Using my web site
Length: | 14 bp
Tm: | 37.8 C
GC: | 35.7 %
Any Dimer: | 0.0
End Dimer: | 0.0
Template Mispriming: | 3.0
Hairpin: | 0.0
3' Stability: | 4.3 ΔG
Penalty: | 28.204

I can see that on the sourceforge web site (https://sourceforge.net/p/primer3/primer3plus/ci/master/tree/) there are some commit (related to Bugs Found by Heidelberg Bioinformatics Course) that are not present here in this git repository.

It is possible to merge those versions? Do I need to submit a PR? How can I get the same results as www.bioinformatics.nl web site? thank you.

FredericBGA commented 2 years ago

Hi,

ok, I've found how to get the same results, I need to load the right settings p3 V1.1.4 def

So what about the small bugs that are only fixed on sourceforge?

FredericBGA commented 2 years ago

Hello

I've use "Primer_Check" with this primer TTCTCCTTTGGGCCGTG on https://www.bioinformatics.nl/cgi-bin/primer3plus/primer3plus.cgi.

There is a warning regarding Left primer is unacceptable: High 3' stability
And nothing about the length, even if in "General Settings" the min length is set to 18

Using my web site and this git repo, with the same primer.

No warning regarding the stability.
A warning complaining about the size Error: Specified right primer < PRIMER_MIN_SIZE as in "General Settings" the min length is set to 18

Do I miss the stability warning? And why there is no issue detected around the primer length on https://www.bioinformatics.nl/cgi-bin/primer3plus/primer3plus.cgi? Which site is the best?

Thank you.

Fred

untergasser commented 2 years ago

Hi,

so let me explain. www.bioinformatics.nl was the first Primer3Plus release we prepared. It is not under my control and I think it is now 10 years behind and therefore I can not see into the settings or comment on the parameters. The latest version is on dev.primer3plus.com. I will within a few month also update primer3plus.com, which is a 3 year old version, to the same version as dev.primer3plus.com. A one year old version is available on https://www.gear-genomics.com/primer3plus/

In future, https://www.gear-genomics.com/primer3plus/ and www.primer3plus.com and dev.primer3plus.com will have the same version now available at dev.primer3plus.com.

If I continue some developments, will move on dev.primer3plus.com to try things out. This server is cutting edge. Once it is stable and I like my changes, I will sync https://www.gear-genomics.com/primer3plus/ and www.primer3plus.com to this version.

I hope that helps.

The sourceforge additions are in the github repo, just way back. With the release tomorrow, I will sync them to the same level.

Best,

Andreas

FredericBGA commented 2 years ago

Yes! Perfect. Thank you Andreas.

Fred