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# MEGABLAST default substitution scores.
# For the default gap scores, as used for MEGABLAST on NCBI Web
# BLAST, The BLAST documentation shows gap costs a = 0 for opening
# a gap, and b = 2.5 for each letter in the gap, and defines the
# total score of a gap of k residues as -(a + b*k). In contrast,
# Biopython follows the definition given in "Biological Sequence
# Analysis" (Durbin et al., 1998), for which the total score of a
# gap of k residues is -d - e * (k - 1), where d is the gap-open
# penalty and e is the gap-extend penalty. Biopython uses -d as
# the gap open score and -e as the gap extend penalty:
# gap open score: -2.5
# gap extend score: -2.5
# with the substitution matrix below, as the MEGABLAST score parameters.
A T G C S W R Y K M B V H D N
A 1 -2 -2 -2 -2 -1 -1 -2 -2 -1 -2 -1 -1 -1 -1
T -2 1 -2 -2 -2 -1 -2 -1 -1 -2 -1 -2 -1 -1 -1
G -2 -2 1 -2 -1 -2 -1 -2 -1 -2 -1 -1 -2 -1 -1
C -2 -2 -2 1 -1 -2 -2 -1 -2 -1 -1 -1 -1 -2 -1
S -2 -2 -1 -1 -1 -2 -1 -1 -1 -1 -1 -1 -1 -1 -1
W -1 -1 -2 -2 -2 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1
R -1 -2 -1 -2 -1 -1 -1 -2 -1 -1 -1 -1 -1 -1 -1
Y -2 -1 -2 -1 -1 -1 -2 -1 -1 -1 -1 -1 -1 -1 -1
K -2 -1 -1 -2 -1 -1 -1 -1 -1 -2 -1 -1 -1 -1 -1
M -1 -2 -2 -1 -1 -1 -1 -1 -2 -1 -1 -1 -1 -1 -1
B -2 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1
V -1 -2 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1
H -1 -1 -2 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1
D -1 -1 -1 -2 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1
N -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1
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