Utility For Downloading Sequences From A List Of Mixed Database Keys

Question

[Will]

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

Answer 1

[Will]

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.

Answer 2

[Andrew Su]

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):

• http://mygene.info/query?q=ENSP00000450983
• http://mygene.info/query?q=DQ890598
• http://mygene.info/query?q=1PF8

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

• http://mygene.info/gene/1017

[Will]

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

[Will]

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.

[Andrew Su]

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.