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schwede
openstructure
Commits
072f2500
Commit
072f2500
authored
4 years ago
by
Studer Gabriel
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simplify docu
parent
b5083323
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modules/bindings/pymod/hhblits3.py
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modules/bindings/pymod/hhblits3.py
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072f2500
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@@ -523,14 +523,6 @@ class HHblits:
def
BuildQueryMSA
(
self
,
nrdb
,
options
=
{},
a3m_file
=
None
,
assign_ss
=
True
):
"""
Builds the MSA for the query sequence.
This function directly uses hhblits of hhtools. While in theory it would
be possible to do this by PSI-blasting on our own, hhblits is supposed
to be faster. Also it is supposed to prevent alignment corruption. The
alignment corruption is caused by low-scoring terminal alignments that
draw the sequences found by PSI-blast away from the optimum. By removing
these low scoring ends, part of the alignment corruption can be
suppressed.
The produced A3M file can be parsed by :func:`ParseA3M`. If the file was
already produced, hhblits is not called again and the existing file path
is returned (neglecting the *assign_ss* flag!!!).
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