[Biopython] using prosite

[David Shin]

Hi Again,

I'm trying to find motifs in a group of proteins using prosite via
biopython.

I've tried to copy what's in the tutorial (pg 152-153) into a script to get
started.

If I run it on my test sequence I get nothing, so I assume the default is
to "exclude motifs with a high probability of occurrence from the scan"
like on the website.

So I'm trying to substitute some flag to turn off this feature, or to just
scan for specific motifs, ie. PS00001 Asn-Glycosylation, but have had no
luck.

Any suggestions on syntax here?

Below is a basic script where I tried to give a specific motif:

from Bio.ExPASy import ScanProsite

sequence =
"MSQHLLLLILLSLLLLSLLLLHKPISATTIIQKFKEAPQFYNSADCPLIDDSESDDDVVAKPIFCSRRAVHVAMTLDAAYIRGSVAAVLSVLQHSSCPENIVFHFVASASADASSLRATISSSFPYLDFTVYVFNVSSVSRLISSSIRSALDCPLNYARSYLADLLPPCVRRVVYLDSDLILVDDIAKLAATDLGRDSVLAAPEYCNANFTSYFTSTFWSNPTLSLTFADRKACYFNTGVMVIDLSRWREGAYTSRIEEWMAMQKRMRIYELGSLPPFLLVFAGLIKPVNHRWNQHGLGGDNFRGLCRDLHPGPVSLLHWSGKGKPWARLDAGRPCPLDALWAPYPDPDPDDLLQTPFALDS"

handle = ScanProsite.scan(seq=sequence, accession=PS00001)

result = ScanProsite.read(handle)

print type(result)

print len(result)

print result[0]

print result[1]

Thanks!
Dave