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) 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.
Public Member Functions