Forum: Looking For More Data To Build A Bacterial Primer Database
gravatar for vijay
5.2 years ago by
vijay1.3k wrote:

Dear All,

I am in the process of collecting various bacterial(species specific) primer sequences for the 16s rRNA gene. Am trying to a make a local database out of them. I am going through various journals and articles to get some data. Also I thought I would post in this forum.

Please provide me with some references or some validated primer sequences .

Thanks for your help.

metagenomics forum primer • 2.1k views
ADD COMMENTlink modified 4.7 years ago by Michael Dondrup43k • written 5.2 years ago by vijay1.3k
gravatar for Cliff Beall
5.2 years ago by
Cliff Beall450
Cliff Beall450 wrote:

I think ProbeBase might be what you're looking for. They have both species-specific and universal primers (2663 total):

ADD COMMENTlink written 5.2 years ago by Cliff Beall450

+1 on this. Thanks for the link. I was not aware of this database.

ADD REPLYlink written 5.2 years ago by Josh Herr5.5k
gravatar for Josh Herr
5.2 years ago by
Josh Herr5.5k
University of Nebraska
Josh Herr5.5k wrote:

This would be a very large database, so kudos to you for trying to rein all the information in. Two papers this year stood out for me in this area (but there were lots of 16S papers focusing on different primers): Soergel et al in The ISME Journal and Winsley et al in AEM.

There's a lot of taxonomic discrepancy in some of the primer pairs, so a database with the recorded bacterial diversity using the primers across many samples of different habitats (soil, human microbiome, marine, etc.) would be a valuable contribution.

ADD COMMENTlink written 5.2 years ago by Josh Herr5.5k
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