Question: Get Taxonomy/Organism information from GenBank Ids
0
gravatar for mrtombooker
14 months ago by
mrtombooker0 wrote:

Hi BioStars,

Does anyone have any suggestions for fast ways to retrieve multiple genbank records using a list of genbank ids/accessions? I am interested in getting the Taxonomic and/or Organism fields for a large set of queries. They are blast hits for environmental RNA so could come from a variety of sources. I have a large number of runs (like 20 x 500 ids) so submitting them on the website is not really an option.

I tried the Entrez eSearch software but that is pretty dang slow to submit and download queries, plus I don't want to hammer the NCBI servers any more than I need to.

I have the space to download GenBank if anyone knows of a way to format the files into a form that is quickly queried.

Any help or tips would be appreciated.

blast genbank sequence • 483 views
ADD COMMENTlink modified 14 months ago by natasha.sernova2.4k • written 14 months ago by mrtombooker0
1
gravatar for natasha.sernova
14 months ago by
natasha.sernova2.4k
natasha.sernova2.4k wrote:

Actually this question has been already asked here,

Fetching Genbank Entries For List Of Accession Numbers.

with nice biopython scrips inside as answers.

There are more than one approach described there, read carefully.

ADD COMMENTlink modified 14 months ago • written 14 months ago by natasha.sernova2.4k

Thanks Natasha,

I had tried to find previous answers but I guess I missed this one.

ADD REPLYlink written 14 months ago by mrtombooker0

Below there is it's url:

Fetching Genbank Entries For List Of Accession Numbers.

I've spoilt it a little bit.

*tps://www.biostars.org/p/66921/

Look at the post, it's helpful!

ADD REPLYlink modified 14 months ago • written 14 months ago by natasha.sernova2.4k
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