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

List of all members.

Detailed Description

Stores information about one hsp in an alignment hit.

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)
align_length    Length of the alignment. (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)
query_end       The end 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)
sbjct_end       The end 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

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

Definition at line 102 of file Record.py.

Public Member Functions

def __init__

Public Attributes


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

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