U.S. Department of Energy

Pacific Northwest National Laboratory

Uniprot DAT File Parser

The Uniprot DAT File Parser can read a Uniprot .Dat file and parse out the information for each entry, creating a series of tab delimited text files or creating a FASTA file.

Area of Research: 

Uniprot .Dat files can be obtained from EBI's FTP site. Useful folders include:

See also http://web.expasy.org/docs/userman.html for a list of frequently asked questions concerning Uniprot files.

The tab-delimited files created are:

  • Primary data file, with one line per protein entry in the .DAT file, for example:
Protein_Name Accession Description Sequence_AA_Count MW Organism Phylogeny Accession1
12AH_CLOS4 P21215; RecName: Full=12-alpha-hydroxysteroid dehydrogenase; EC=; Flags: Fragment; 29 2900 Clostridium sp. (strain ATCC 29733 / VPI C48-50) Bacteria; Firmicutes; Clostridia; Clostridiales; Clostridiaceae; Clostridium. P21215
12KD_MYCSM P80438; RecName: Full=12 kDa protein; Flags: Fragment; 24 2766 Mycobacterium smegmatis Bacteria; Actinobacteria; Actinobacteridae; Actinomycetales; Corynebacterineae; Mycobacteriaceae; Mycobacterium. P80438
12S_PROFR Q8GBW6; Q05617; RecName: Full=Methylmalonyl-CoA carboxyltransferase 12S subunit; EC=; AltName: Full=Transcarboxylase 12S subunit; 611 65927 Propionibacterium freudenreichii subsp. shermanii Bacteria; Actinobacteria; Actinobacteridae; Actinomycetales; Propionibacterineae; Propionibacteriaceae; Propionibacterium. Q8GBW6
  • Organism Summary file
Organism Proteins
Acidianus ambivalens 105
Acidianus brierleyi 11
Acidianus hospitalis 2368
Acidianus infernus 3
  • Organism Map file
Protein Organism Strain
F7PIW9_9EURY Halorhabdus tiamatea SARL4B  
F7PNT1_9EURY Halorhabdus tiamatea SARL4B  
Q2FP08_METHJ Methanospirillum hungatei JF-1 strain ATCC 27890 / DSM 864 / NBRC 100397 / JF-1
U1PGF8_9EURY Haloquadratum walsbyi J07HQW1  



Version 1.1.5674; July 15, 2015

Software Instructions: 

Run UniprotDATFileParser_Installer.msi to install the application.  This is a command-line (console) application and thus does not have a GUI.   For more information on using command line applications, see the Command Line Application help page.


All publications that utilize this software should provide appropriate acknowledgement to PNNL and the OMICS.PNL.GOV website. However, if the software is extended or modified, then any subsequent publications should include a more extensive statement, as shown in the Readme file for the given application or on the website that more fully describes the application.



These programs are primarily designed to run on Windows machines. Please use them at your own risk. This material was prepared as an account of work sponsored by an agency of the United States Government. Neither the United States Government nor the United States Department of Energy, nor Battelle, nor any of their employees, makes any warranty, express or implied, or assumes any legal liability or responsibility for the accuracy, completeness, or usefulness or any information, apparatus, product, or process disclosed, or represents that its use would not infringe privately owned rights.

Portions of this research were supported by the NIH National Center for Research Resources (Grant RR018522), the W.R. Wiley Environmental Molecular Science Laboratory (a national scientific user facility sponsored by the U.S. Department of Energy's Office of Biological and Environmental Research and located at PNNL), and the National Institute of Allergy and Infectious Diseases (NIH/DHHS through interagency agreement Y1-AI-4894-01). PNNL is operated by Battelle Memorial Institute for the U.S. Department of Energy under contract DE-AC05-76RL0 1830.

We would like your feedback about the usefulness of the tools and information provided by the Resource. Your suggestions on how to increase their value to you will be appreciated. Please e-mail any comments to proteomics@pnl.gov

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