Question: blasting genome contigs against local SILVA 16S RNA database
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gravatar for robjohn70000
3.6 years ago by
robjohn70000110
Nigeria
robjohn70000110 wrote:

Hi All,

I'm new to bioinformatics and interested in determining the bacteria strains in a collection of bacteria genome contigs. I wonder if is logical and appropriate to create a local SILVA 16S RNA database and then blast (using blastn) the genome contigs against the 16S RNA  database. My main concern is that, will it be logical to blast DNA sequences against RNA sequences in the 16S RNA database.

I welcome some advice. Thanks


 

sequencing blast genome • 1.9k views
ADD COMMENTlink modified 3.6 years ago by marina.v.yurieva400 • written 3.6 years ago by robjohn70000110
0
gravatar for Istvan Albert
3.6 years ago by
Istvan Albert ♦♦ 76k
University Park, USA
Istvan Albert ♦♦ 76k wrote:

if your RNA sequences are represented in the DNA alphabet and then there shouldn't be any problem - that's standard protocol

ADD COMMENTlink written 3.6 years ago by Istvan Albert ♦♦ 76k

Thanks @Istvan. I noticed that the RNA sequences have 'U's in place of 'T's. 
 

ADD REPLYlink written 3.6 years ago by robjohn70000110

NCBI provides taxonomically annotated 16S databases that can be used directly.

ADD REPLYlink written 3.6 years ago by Istvan Albert ♦♦ 76k
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gravatar for marina.v.yurieva
3.6 years ago by
Farmington, CT
marina.v.yurieva400 wrote:

If you haven't done this type of analysis before you might look into developed pipelines: mothur and QIIME. For standard 16S analysis blasting is not very efficient.

ADD COMMENTlink written 3.6 years ago by marina.v.yurieva400

Indeed, for 454 type of data it may work, but for large number of reads such as from MiSeq the process requires a lot of resources

ADD REPLYlink written 3.6 years ago by Istvan Albert ♦♦ 76k

Thank you all very much for your contributions and advice. I will be looking at the the suggested tools.
 

ADD REPLYlink written 3.6 years ago by robjohn70000110
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