blast - Search related sequences in databases
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Blast(query, database, gap_open=11, gap_ext=1, matrix='BLOSUM62', blast_location=None, outfmt=0, filter_low_complexity=True)
Runs a protein vs. protein blast search. The results are returned as a
list of BlastHit instances.
Parameters: |
- query (seq.ConstSequenceHandle) – the query sequence
- database – The filename of the sequence database. Make sure that
formatdb has been run on the database and the <database>.pin file exists.
- matrix – The substitution matrix to be used. Must be one of ‘BLOSUM45’,
‘BLOSUM62’, ‘BLOSUM80’, ‘PAM30’, ‘PAM70’.
- 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.
- 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.
- outfmt – output format, where ‘0’ corresponds to default output (parsed blast output and 1 to raw output)
- filter_low_complexity – Mask off segments of the query sequence that
have low compositional complexity, as determined by the SEG program of
Wootton & Federhen (Computers and Chemistry, 1993)
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ParseBlastOutput(string, seqid_thres=0, evalue_thres=inf)
Parses the blast output and returns a list of BlastHits
setting no seqid_thres or evalue_thres, restores default behaviour without filtering
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class AlignedPatch(aln, bit_score, score, evalue, seqid)
An aligned patch, aka. HSP
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aln
The local alignment. Sequence offset of both sequences in the alignment are
set to the starting position in the query and target sequence, respectively.
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bit_score
The bit score of the HSP
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score
The score of the HSP
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evalue
The E-value of the HSP
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seqid
The sequence identity of the HSP
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class BlastHit(identifier, aligned_patches)
A positive match found by BLAST.
Each blast hit consists of one or more HSPs, encoded by the
AlignedPatch class.
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identifier
The identifier of the matching sequence
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aligned_patches
list of AlignedPatch instances holding the actual HSPs.
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class BlastError(brief, details)
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