Finding 16s DNA Sequence in de novo assembled genome

[cwisch88]

From time to time I find I'm working with a bunch of de novo assemblies. I've been interested in doing some comparative genomics and perhaps making some group-specific 16s rRNA primers.

I'm just wondering if there is an accepted way of extracting 16s DNA from de novo assemblies that I'm just not finding.

I've used BLAST and other Local alignment programs using universal primers, but this doesn't strike me as very efficient and I'm sure I'm not the only one trying do something like this. Can anyone point me toward any papers or personal experience doing something like this.

Thanks!

[boetsie]

You can use a tool like barrnap

http://www.vicbioinformatics.com/software.barrnap.shtml

or RNAmmer

http://www.cbs.dtu.dk/services/RNAmmer/

to predict rRNA locations on your contig sequences.

Boetsie

[cwisch88]

Thanks

I will definitely check these out!

[rhinoceros]

Blast the contigs against a 16S db?

[cwisch88]

Blast the contigs against a 16S db?

That is a very straightforward approach and I have done that in past. I was just wondering if there was something that could quickly extract the sequences without reinventing the wheel.

It looks like the barrnap program does a quick annotation and then I can use something like bedtools to extract the sequences using the produced GFF.