how to get database of plants in FASTA format from uniprot

Question

[majeedaasim]

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

Answer 1

[Andrzej Zielezinski]

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.

[majeedaasim]

thanks for the the help

[Andrzej Zielezinski]

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

Answer 2

[ricardoguerreiro2121]

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

[dimitrischat]

but this is .dat file not fasta

[GenoMax]

Those files are in UniProtKB format.

[dimitrischat]

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 ?

[ricardoguerreiro2121]

Hey, you just got an answer to that bellow: Python script swissprot2fasta.py) from MakerP (https://github.com/bioxfu/MakerP) to convert .dat to .fasta

Answer 3

[shzhang]

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