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Fetch Sequences from SwissProt with Bio.ExPASy.get_sprot_raw()
How to Fetch Sequences from SwissProt with Bio.ExPASy.get_sprot_raw() function?
✍: FYIcenter.com
SwissProt with Bio.ExPASy.get_sprot_raw() function allows you to fetch protein
sequences from SwissProt database.
Here is an example on how to Fetch Sequences from SwissProt.
fyicenter$ python >>> from Bio import ExPASy >>> from Bio import SeqIO >>> with ExPASy.get_sprot_raw("O23729") as handle: ... seq_record = SeqIO.read(handle, "swiss") ... >>> print(seq_record) ID: O23729 Name: CHS3_BROFI Description: RecName: Full=Chalcone synthase 3; EC=2.3.1.74; AltName: ... Database cross-references: EMBL:AF007097, AlphaFoldDB:O23729, SMR:O23729, ... Number of features: 2 /molecule_type=protein /accessions=['O23729'] /protein_existence=2 /date=15-JUL-1999 /sequence_version=1 /date_last_sequence_update=01-JAN-1998 /date_last_annotation_update=14-DEC-2022 /entry_version=80 /gene_name=[{'Name': 'CHS3'}] /organism=Bromheadia finlaysoniana (Orchid) /taxonomy=['Eukaryota', 'Viridiplantae', 'Streptophyta', 'Embryophyta', ... /ncbi_taxid=['41205'] /comment=FUNCTION: The primary product of this enzyme is 4,2',4',6'- ... CATALYTIC ACTIVITY: Reaction=4-coumaroyl-CoA + 2 H(+) + 3 malonyl-CoA = ... PATHWAY: Secondary metabolite biosynthesis; flavonoid biosynthesis. SIMILARITY: Belongs to the thiolase-like superfamily. Chalcone/stilbene ... /references=[Reference(title='Molecular cloning and sequence analysis of ... /keywords=['Acyltransferase', 'Flavonoid biosynthesis', 'Transferase'] Seq('MAPAMEEIRQAQRAEGPAAVLAIGTSTPPNALYQADYPDYYFRITKSEHLTELK...GAE') >>> print(seq_record.features[0]) type: CHAIN location: [0:394] id: PRO_0000215956 qualifiers: Key: note, Value: Chalcone synthase 3
⇒ Scan Prosite Databas with Bio.ExPASy.ScanProsite.scan()
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