Question: Local blast limit query search by GI list?
0
gravatar for milt0n
3.1 years ago by
milt0n0
milt0n0 wrote:

Hi All,  

I am trying to blast a file that contains about 42k fasta sequences against a local blast database (nt), and I would like to restrict the search space. I read that a common way to do that is to restrict the search using "gi" (see command line below).

My question is: How would you go about to obtain a list of gi striclty for bacteriophage related nucleotide sequences? What I have done before is going to the NCBI nucleotide database, searching for "bacteriophage", then exporting the list of results to a gi file. But I am not sure if this is the way to do it as I get also other results (other microbes). 

Or am I going about this wrong?

Thanks for you help,

C

$ blastn -db nt -gilist list.gi -query seq.fasta -out blast_results.txt
blast latest bacteriophage • 1.5k views
ADD COMMENTlink modified 3.1 years ago by genomax64k • written 3.1 years ago by milt0n0
3
gravatar for genomax
3.1 years ago by
genomax64k
United States
genomax64k wrote:

That is the right way to do this.  Getting all viral genomes and parsing out bacteriophage gi's may be preferred option. I see 1700+ entries for phages.

$ grep "phage" viral.1.1.genomic.fna | awk -F "|" '{print $2}'  > phage_gi_list

should do it.

You could try the taxonomy ID route to get a more restricted set of gi: http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=38018 I am not sure if that option gives you all bacteriophages though.

 

ADD COMMENTlink modified 3.1 years ago • written 3.1 years ago by genomax64k

Thanks, the first link is indeed too restrictive, but I see what you mean. I'll explore a bit further.

C

ADD REPLYlink written 3.1 years ago by milt0n0
1

Go with the viral genomes option. I will move it up in the post above.

ADD REPLYlink written 3.1 years ago by genomax64k
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