Class HSP
source code
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 (int) if using the XML parser.
Tuple of numer of identities/total aligned (int, int)
if using the (obsolete) plain text parser.
positives Number of positives (int) if using the XML parser.
Tuple of numer of positives/total aligned (int, int)
if using the (obsolete) plain text parser.
gaps Number of gaps (int) if using the XML parser.
Tuple of numer of gaps/total aligned (int, int) if
using the (obsolete) plain text parser.
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
in TBLASTX.
Also, for negative frames, the sequence numbering starts from
query_start and counts down.