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how to get database of plants in FASTA format from uniprot

I need to align my transcripts with database of plants that I downloaded from UniProt. but it is in txt format and I require FASTA format. PLease suggest a solution. Do I have to retrieve the data from other source?

Thanks

blast
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updated by shzhang • shzhang • written by majeedaasim • majeedaasim

3 answers

  1. Go to UniProt website
  2. Search for: taxonomy:viridiplantae
  3. Click on the Download button:
    • Check Download all
    • Select Format: FASTA
    • Check Compressed
    • Click GO.
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written by Andrzej Zielezinski Andrzej Zielezinski

Sure! If I answered your question, please mark my post as accepted by clicking on the thick (check sign) icon.

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written by Andrzej Zielezinski Andrzej Zielezinski

Hi,

The accepted answer is not optimal. The entire plant database is huge and takes a long time to download via browser.

After a long time, I found the best solution:

wget ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/taxonomic_divisions/uniprot_trembl_plants.dat.gz

Took me 2 days search to find this link. It should be easier to find!

Cheers, Ricardo

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written by ricardoguerreiro2121 ricardoguerreiro2121

but this is .dat file not fasta

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written by dimitrischat dimitrischat

Those files are in UniProtKB format.

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written by GenoMax GenoMax

yea dont know if you can use them (.dat files) for blastp in terminal. Or you can?

edit: is there a way to convert .dat file to .fasta ?

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written by dimitrischat dimitrischat

In case others need to retrieve the plant uniprot sprot database, one can download the .dat file (uniprot_sprot_plants.dat.gz) from ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/taxonomic_divisions/, and then use a Python script (swissprot2fasta.py) from MakerP (https://github.com/bioxfu/MakerP) to convert .dat to .fasta

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written by shzhang • shzhang

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