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Commit 072f2500 authored by Studer Gabriel's avatar Studer Gabriel
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simplify docu

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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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