Runs a protein vs. protein blast search. The results are returned as a
list of :class:`BlastHit` instances.
:param query: the query sequence
:type query: :class:`seq.ConstSequenceHandle`
:param database: The filename of the sequence database. Make sure that
formatdb has been run on the database and the <database>.pin file exists.
:param matrix: The substitution matrix to be used. Must be one of 'BLOSUM45',
'BLOSUM62', 'BLOSUM80', 'PAM30', 'PAM70'.
:param gap_open: Gap opening penalty. Note that only a subset of gap opening
penalties is supported for each substitutition matrix. Consult the blast
docs for more information.
:param gap_ext: Gap extension penalty. Only a subset of gap extension
penalties are supported for each of the substitution matrices. Consult the
blast docs for more information.
Definition at line 85 of file blast.py.
