Question: How To Download Swiss-Prot .Dat File From Uniprot
gravatar for kevinjspring
5.5 years ago by
United States
kevinjspring20 wrote:

I have been trying to use Biopython to parse out certain domains from proteins and it was suggested to use the Bio.SwissProt module. Unfortunately, I don't see any SwissProt data files available on UniProt. The only available file formats are GGF, FASTA, XML, and TXT. Anyone know how I can get access to the Swiss-Prot file format?

python biopython uniprot • 6.7k views
ADD COMMENTlink modified 3.0 years ago by naseeb_qau@yahoo.com0 • written 5.5 years ago by kevinjspring20

TXT is what you want.

ADD REPLYlink written 5.5 years ago by Neilfws48k

I did a slight work around where I pulled the accession numbers from UniProt and then used the Biopython module ExPASy to pull the data.

ADD REPLYlink written 5.5 years ago by kevinjspring20
gravatar for Hamish
5.5 years ago by
Hamish3.1k wrote:

The "text" files (also known as 'dat' files) are the files in UniProtKB/SwissProt format, so you can fetch these with:

wget '*.dat.gz'

or using one of the many mirrors:

wget '*.dat.gz'

Note: the UniProtKB/TrEMBL file is large (approx. 20GB compressed and about 110GB uncompressed) so you will likely only want to download this if you need to. See Why is UniProtKB composed of 2 sections, UniProtKB/Swiss-Prot and UniProtKB/TrEMBL? for an overview of the differences between UniProtKB/SwissProt and UniProtKB/TrEMBL.

If you need the whole database fetches like the above are recommended.

UniProt also provide subsets of the database based on:

Which may be more appropriate if you are only interested in certain organisms.

For specific entries, where you already have a list of identifiers or accessions, the various web services providing access to the UniProtKB data are more appropriate. For example:

ADD COMMENTlink written 5.5 years ago by Hamish3.1k
gravatar for Prakki Rama
5.5 years ago by
Prakki Rama2.2k
Prakki Rama2.2k wrote:

Hi, is this what you are looking for?

ADD COMMENTlink modified 5.5 years ago • written 5.5 years ago by Prakki Rama2.2k

No, it seems like I need to use the ExPASy module to pull the records from the ExPASy database

ADD REPLYlink written 5.5 years ago by kevinjspring20
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