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steineggerlab / foldseek

Foldseek enables fast and sensitive comparisons of large structure sets.
https://foldseek.com
GNU General Public License v3.0
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link target ids to real name #20

Open lalalagartija opened 2 years ago

lalalagartija commented 2 years ago

Hi, Is there a way to request NCBI or Uniprot accessions and/or the functions of the target proteins using foldseek api ?

with the python command : result = get('https://search.foldseek.com/api/result/' + ticket['id'] + '/0').json() I get the target accession only. If not, is there a way to batch request functions with alphafold database accessions ?

Thank you for this great tool by the way

igortru commented 1 year ago

probably,you will be interested I have created map (july 21,2022) from sequence crc64 (GCP bigquery deepmind AF metainfomation table) to alphafold/uniprot and genbank accessions.

map contain ~2G rows because uniprot/genbank/alphafold accessions spaces are very redundant zipped 13Gb file located on https://ftp.ncbi.nlm.nih.gov/genomes/Viruses/AlphaFold2NR.map.gz