Enquiry

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Marwa Said

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Mar 22, 2017, 9:15:25 AM3/22/17
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Hi biogps team,

 Please, i want to ask how can convert 6000 records of protein_ID to sequences in FASTA format.

thanks & best regards 
 

Eng. Marwa S. Hassan MSc.
Assistant Researcher
Information and systems Department
Engineering division 
National Research Center (NRC)
Cairo, Egypt

G Tsueng

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Mar 22, 2017, 4:54:17 PM3/22/17
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Hi,

BioGPS does not store FASTA files nor are there any plugins currently available for handling those (that I'm aware of anyway).  You could use MyGene.info (available as a python package, R package, and API) to batch convert your protein IDs to Uniprot IDs (it's not clear what protein id's you have).  Then use Uniprot's RESTful API to retrieve the FASTA files. 

best wishes,
ginger
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