Question: Can you combine nt and WGS nucleotide databases for a BLAST search and make it non redundant?
0
gravatar for lauraeiv
3.5 years ago by
lauraeiv0
European Union
lauraeiv0 wrote:

Hi,

I am a beginner in bioinformatics and I want to blast a nucleotide sequence against a nucleotide database but the nucleotide collection(nt) database excludes WGS which i would like to include.

Is there a way I can join these two databases to give me the output i want while remaining non redundant?

If this is even possible, can you do this using web blast rather than the command line?

myposts blast blast database • 1.5k views
ADD COMMENTlink modified 3.5 years ago by Brian Bushnell16k • written 3.5 years ago by lauraeiv0
1
gravatar for pld
3.5 years ago by
pld4.8k
United States
pld4.8k wrote:

The WGS database contains 'in progress' genomes, since people might be working on the same organisms, similar strains, and metagenomic samples, there's plenty of opportunity for the same thing to show up.

You could possibly using the nt database, but whatever redundant sequences not presently in nt wouldn't be removed from WGS.

Either way, I don't think WWWBLAST will work.

ADD COMMENTlink written 3.5 years ago by pld4.8k

Thanks for that. I am doing both a nucleotide and protein blast so I am hoping to get the same genomes in the nucleotide as I am with the nr/nt protein database.

Is it possible to do with command line? I am very stuck for time so I dont think this is an option for me anyway

ADD REPLYlink modified 3.5 years ago • written 3.5 years ago by lauraeiv0
1
gravatar for Brian Bushnell
3.5 years ago by
Walnut Creek, USA
Brian Bushnell16k wrote:

nt is already internally redundant.  You can remove redundancy from one or more fasta files using Dedupe, part of the BBMap package, like this:

dedupe.sh in=file1.fa,file2.fa out=deduped.fa

ADD COMMENTlink written 3.5 years ago by Brian Bushnell16k
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