Logo Search packages:      
Sourcecode: python-biopython version File versions

Bio::Blast::Record::HSP Class Reference

List of all members.


Detailed Description

Stores information about one hsp in an alignment hit.

Members:
score           BLAST score of hit.  (float)
bits            Number of bits for that score.  (float)
expect          Expect value.  (float)
num_alignments  Number of alignments for same subject.  (int)
identities      Number of identities/total aligned.  tuple of (int, int)
positives       Number of positives/total aligned.  tuple of (int, int)
gaps            Numer of gaps/total aligned.  tuple of (int, int)
strand          Tuple of (query, target) strand.
frame           Tuple of 1 or 2 frame shifts, depending on the flavor.

query           The query sequence.
query_start     The start residue for the query sequence.  (1-based)
match           The match sequence.
sbjct           The sbjct sequence.
sbjct_start     The start residue for the sbjct sequence.  (1-based)

Not all flavors of BLAST return values for every attribute:
          score     expect     identities   positives    strand  frame
BLASTP     X          X            X            X
BLASTN     X          X            X            X          X
BLASTX     X          X            X            X                  X
TBLASTN    X          X            X            X                  X
TBLASTX    X          X            X            X                 X/X

Note: for BLASTX, the query sequence is shown as a protein sequence,
but the numbering is based on the nucleotides.  Thus, the numbering
is 3x larger than the number of amino acid residues.  A similar effect
can be seen for the sbjct sequence in TBLASTN, and for both sequences
in TBLASTX.

Also, for negative frames, the sequence numbering starts from
query_start and counts down.

Definition at line 98 of file Record.py.


Public Member Functions

def __init__

Public Attributes

 bits
 expect
 frame
 gaps
 identities
 match
 num_alignments
 positives
 query
 query_start
 sbjct
 sbjct_start
 score
 strand

The documentation for this class was generated from the following file:

Generated by  Doxygen 1.6.0   Back to index