Extraction of 16S rRNA gene

Question

[glady]

how can we extract 16s rrna from an assembled genome. Can we extract it from RAST ? If yes, then how ?

[natasha.sernova]

See this article:

Direct 16S rRNA-seq from bacterial communities: a PCR-independent approach to simultaneously assess microbial diversity and functional activity potential of each taxon...

http://www.nature.com/articles/srep32165, it cites RAST (18)

http://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-9-386

Then go here:

http://molbiol-tools.ca/molecular_biology_freeware.htm and find myRAST. url is below:

http://blog.theseed.org/servers/presentations/t1/running-a-job-with-the-desktop-rast.html

[WouterDeCoster]

Not an answer to the question. OP has an assembled genome and wants to find the 16S rRNA sequence from that assembled genome. OP isn't looking for a wet lab approach to sequence the 16S rRNA.

[glady]

I want an in-silico method, by which I can pool out the 16S rRNA gene from the genome.

[natasha.sernova]

OK, I can suggest another way. Find any bacterial 16S rRNA gene from NCBI

( www.ncbi.nlm.nih.gov )

and run MAUVE (see the post below for MAUVE link)

A: Bacterial genome comparison .

16S rRNA genes are very similar between bacteria; the same taxon as your bacterium'

is better for an initial choice, but it doesn’t really matter.

Answer 1

[natasha.sernova]

See this post to extract all bacterial 16S rRNA

A: How To Download The16S Rdna Sequences Of All The Bacterial Species?

or this post - to extract a single one:

How To Identify The 16S Rrna Gene Sequence In A Genome

This post may also be helpful:

Fastest and memory efficient tool for 16S RNA counts