Data Structures | Functions
ost.bindings.blast Namespace Reference

Data Structures

class  AlignedPatch
class  BlastHit
class  BlastError


def ParseBlastOutput
def Blast

Function Documentation

def ost.bindings.blast.Blast (   query,
  gap_open = 11,
  gap_ext = 1,
  matrix = 'BLOSUM62',
  blast_location = None 
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

def ost.bindings.blast.ParseBlastOutput (   string)
Parses the blast output and returns a list of BlastHits

Definition at line 26 of file