Question: Utility For Downloading Sequences From A List Of Mixed Database Keys
1
gravatar for Will
7.5 years ago by
Will4.5k
United States
Will4.5k wrote:

I have a large list of sequence IDS that I need to download the AA sequences for. Its a mixed bag of Uniprot, Refseq, and NCBI Protein Accession. And the IDs are to a collection of organisms (mostly human but some HIV, HCV, rat, etc.)

Does anyone know of a webtool that can handle a mixed lists of ids and convert them to a single database? I know I can use biomart (or some other tool) to convert everything to a single ID system but I was wondering if there are any tools that can do that step for me.

Thanks,

-Will

database sequence download • 1.4k views
ADD COMMENTlink modified 7.5 years ago by Andrew Su4.8k • written 7.5 years ago by Will4.5k
2
gravatar for Will
7.5 years ago by
Will4.5k
United States
Will4.5k wrote:

Well, in-case anyone comes across this post later I've landed on using EBI's PICR tool. Which has a nice REST interface and can deal with seemingly any accession you throw at it.

So I use PICR to convert all of the IDS to SWISSPROT and then download the sequences from there.

ADD COMMENTlink written 7.5 years ago by Will4.5k
1
gravatar for Andrew Su
7.5 years ago by
Andrew Su4.8k
San Diego, CA
Andrew Su4.8k wrote:

I suspect you're looking for a full web-site to do your conversion, but if you're willing to do some simple parsing you could use our ID-resolution web service at http://mygene.info. For example, these URLs all resolve to the same gene (CDK2, Entrez Gene 1017):

From there, you can get everything you'd want to know by querying by Entrez Gene ID

ADD COMMENTlink written 7.5 years ago by Andrew Su4.8k

That's a great service. If only it it supported all of the organisms I needed.

ADD REPLYlink written 7.5 years ago by Will4.5k

Since you have the source-code public I'll just make my own service ... that way I don't have to blast your website with millions of queries.

ADD REPLYlink written 7.5 years ago by Will4.5k

my guess is that you've already figured it out, but let me know if you need any help adding new organisms to your instance.

ADD REPLYlink written 7.4 years ago by Andrew Su4.8k
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