Question

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

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Entering edit mode

11.3 years ago

vijay ★ 1.6k

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 primer • 4.2k views

ADD COMMENT • link updated 13 months ago by Ram 43k • written 11.3 years ago by vijay ★ 1.6k

score 3 · Answer 1 · 2012-12-14

3

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11.3 years ago

Cliff Beall ▴ 470

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/

ADD COMMENT • link 11.3 years ago by Cliff Beall ▴ 470

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

ADD REPLY • link 11.3 years ago by Josh Herr 5.8k

score 2 · Answer 2 · 2012-12-14

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.