Question: Extraction of 16S rRNA gene
0
gravatar for glady
2.9 years ago by
glady260
glady260 wrote:

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

genome • 2.2k views
ADD COMMENTlink modified 2.9 years ago by natasha.sernova3.6k • written 2.9 years ago by glady260

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

ADD REPLYlink modified 2.9 years ago • written 2.9 years ago by natasha.sernova3.6k
1

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.

ADD REPLYlink written 2.9 years ago by WouterDeCoster42k

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

ADD REPLYlink written 2.9 years ago by glady260

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.

ADD REPLYlink modified 2.9 years ago • written 2.9 years ago by natasha.sernova3.6k
0
gravatar for natasha.sernova
2.9 years ago by
natasha.sernova3.6k
natasha.sernova3.6k wrote:

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

ADD COMMENTlink modified 2.9 years ago • written 2.9 years ago by natasha.sernova3.6k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 976 users visited in the last hour