QB9.1 PTMs
This repo contains the scripts I made to extract PTMs from a .xml.gz SwissProt-Uniprot database file, and put them into a sqlite DB.
Obtain such file from, for example, one of the following sites:
- ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/complete/
- https://www.uniprot.org/downloads
They use SQLalchemy to create and clean the database, stored in SQLite format.
Execute in order, starting by the declarePTMdb.py script.
Disclaimer: it may not be pretty, nor well documented :)
sqlalchemy
Bio
PTMs are defined at https://www.uniprot.org/help/sequence_annotation as "Amino acid modifications".
We count:
- 'modified residue'
- 'cross-link'
- 'disulfide bond'
- 'lipid moiety-binding region'
- 'glycosylation site'
We skip:
- Non-standard residue