how can we extract 16s rrna from an assembled genome. Can we extract it from RAST ? If yes, then how ?
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)
Then go here:
http://molbiol-tools.ca/molecular_biology_freeware.htm and find myRAST. url is below:
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.
I want an in-silico method, by which I can pool out the 16S rRNA gene from the genome.
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.
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
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