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?
for the the help
Sure! If I answered your question, please mark my post as accepted by clicking on the thick (check sign) icon.
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:
Took me 2 days search to find this link. It should be easier to find!
but this is .dat file not fasta
Those files are in UniProtKB format.
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 ?
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
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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