This is a test version of Biostars. For the public version, visit https://www.biostars.org.
Software to find Molecular IDs

Hi,

I am trying to identify unique regions in several bacterial genomes for strain specific identification. I have been using nucmer (mummer wrapper), mauveAligner and BLAST so far.

Is there any whole genome alignment tool best suited to this?

Thanks.

genome alignment
• 157 views • link
written by 112498262 • 112498262

1 answer

I am not sure you need any whole genome alignment tool for that.

The ID you need is 16S rRNA, it is called a 'bacterial signature'

See this article from 2012.

Introducing EzTaxon-e: a prokaryotic 16S rRNA gene sequence database with phylotypes that represent uncultured species

http://www.microbiologyresearch.org/docserver/fulltext/ijsem/62/3/716_ijs038075.pdf?expires=1530898179&id=id&accname=guest&checksum=E08D5AC87C775645C6FDDD32C47D5155

If it is not enough, see this post Extraction of 16S rRNA gene and some comments around.

At the right panel of the page there are a lot of useful links as well.

• 1 views • link
written by natasha.sernova natasha.sernova

Log in to answer this question.

More posts like this