Question: How to query nr database using a list of GI numbers to get xml files?
0
gravatar for grayapply2009
4.7 years ago by
grayapply2009220
United States
grayapply2009220 wrote:

I have a list of GI or Accession numbers. Now I want to query the nr database to get xml files for annotation purpose. How do I do this?

annotation blast xml gi latest • 1.5k views
ADD COMMENTlink modified 4.7 years ago by apt.university70 • written 4.7 years ago by grayapply2009220
2

seach this site for : NCBI efetch

ADD REPLYlink written 4.7 years ago by Pierre Lindenbaum130k
1
gravatar for apt.university
4.7 years ago by
United States
apt.university70 wrote:

The nr database is a collection of protein sequences. Are you interested in extracting the protein sequences associated you list of GIs? If so, you can use Batch Entrez (http://www.ncbi.nlm.nih.gov/sites/batchentrez). From the drop down list select protein. Upload your list and click retrieve.

ADD COMMENTlink modified 9 months ago by RamRS30k • written 4.7 years ago by apt.university70

I'm trying to use blast2go to annotate my sequences. Blast2go accepts xml files from the local nr blast. I'm just wondering if it is possible to get xml files with just GI numbers.

ADD REPLYlink written 4.7 years ago by grayapply2009220

Hi @grayapply2009

I am still not very clear as to what you want to do. Did you run blast locally? What are the GI or accession numbers you refer to in the first post?

If you are running blast on the command line, you can generate the output as XML using the -outfmt 5 parameter. You can then feed that output to blast2GO.

Also, nr is not a good source of GO annotations. Perhaps start with a well annotated DB, such as SwissProt or Trembl.

ADD REPLYlink modified 9 months ago by RamRS30k • written 4.7 years ago by apt.university70

Thanks, my friend. I'll try that.

ADD REPLYlink written 4.7 years ago by grayapply2009220
1
gravatar for apt.university
4.7 years ago by
United States
apt.university70 wrote:

If you are annotating trancriptomics data, see the very helpful Trinotate documentation https://trinotate.github.io/

ADD COMMENTlink modified 9 months ago by RamRS30k • written 4.7 years ago by apt.university70

That's a good one, thanks.

ADD REPLYlink written 4.7 years ago by grayapply2009220
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