Scan Prosite Database with Bio.ExPASy.ScanProsite.scan()

Q

How to Scan Prosite Database with Bio.ExPASy.ScanProsite.scan() function?

✍: FYIcenter.com

A

Bio.ExPASy.ScanProsite.scan() function allows to scan the Prosite database with a given sequence.

Here is an example on how to Scan Prosite Database.

fyicenter$ python 
>>> from Bio.ExPASy import ScanProsite

>>> sequence = (
...   "MEHKEVVLLLLLFLKSGQGEPLDDYVNTQGASLFSVTKKQLGAGSIEECAAKCEEDEEFT"
...   "CRAFQYHSKEQQCVIMAENRKSSIIIRMRDVVLFEKKVYLSECKTGNGKNYRGTMSKTKN"
... )
>>> handle = ScanProsite.scan(seq=sequence)

>>> result = ScanProsite.read(handle)
>>> len(result)
1

>>> result[0]
{'sequence_ac': 'USERSEQ1', 'start': 16, 'stop': 98, 'signature_ac': 'PS50948', 'score': '8.873', 'level': '0'}

⇒ Read Sequence Alignments with Bio.AlignIO

⇐ Fetch Sequences from SwissProt with Bio.ExPASy.get_sprot_raw()

⇑ Biopython - Tools for Biological Computation

⇑⇑ OBF (Open Bioinformatics Foundation) Tools

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