blast - Search related sequences in databases

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 according to the value of the outfmt parameter.

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 string 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)

Return type:

BlastHit (with outfmt=0) or str (with outfmt=1)

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

class AlignedPatch(aln, bit_score, score, evalue, seqid)

An aligned patch, aka. HSP

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.

Type:

AlignmentHandle

bit_score

The bit score of the HSP

score

The score of the HSP

evalue

The E-value of the HSP

seqid

The sequence identity of the HSP

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.

identifier

The identifier of the matching sequence

aligned_patches

list of AlignedPatch instances holding the actual HSPs.

class BlastError(brief, details)