Forum:Looking For More Data To Build A Bacterial Primer Database

Question

[vijay]

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.

Answer 1

[Cliff Beall]

I think ProbeBase might be what you're looking for. They have both species-specific and universal primers (2663 total): http://www.microbial-ecology.net/probebase/

[Josh Herr]

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

Answer 2

[Josh Herr]

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.