Sequence Comparison.pdf

Index 209
heuristic, 85
progressive, 85
multiple spaced seeds, 114
MUMmer, 62
MUSCLE, 88
Needleman-Wunsch algorithm, 9, 60
non-hit probability, 94
optimal alignment, 9, 37, 38, 41, 50
optimal local alignment scores
λ, K, 132
gapped, 134
ungapped, 121, 132, 138
P-value, 128, 130, 133, 134, 141, 144
pairwise alignment, 11, 35, 195
PAM unit, 150
PAM120, 158, 169
PAM250, 138, 158, 166
PAM30, 141, 158, 167
PAM70, 141, 158, 168
PatternHunter, 75
PipMaker, 62
position-specific substitution matrix, 87
problem
exact word match, 64
Fibonacci number, 25
global alignment, 9, 38
local alignment, 10, 42
longest common subsequence, 9, 30
longest increasing subsequence, 27
maximum-sum segment, 26, 70
sorting, 22
progressive alignment, 85
protein, 174
PSI-BLAST, 73
PSSM, 73
random
sequence, 12
variables, 178
covariance, 185
discrete, 178, 179
mean, 183
standard deviation, moment, 185
variance, 185
walk, 191
recurrence, 24
relation, 94
system, 95, 97
renewal
theorem, 126, 192
theory, 191
restricted affine gap penalties, 48
RNA, 173
score
alignment, 8, 37, 83
distance, 9, 57
similarity, 9, 37
sum-of-pairs, 11, 83
scoring
matrix, 7, 37
compositional adjustment, 158
general form, 155
selection, 157
valid, 156
scheme, 8, 37, 38
system, 8
seed
consecutive, 92, 94, 95, 100–104, 112
hit, 77, 95
length, 93
multiple, 114
PatternHunter, 112
selection, 110
spaced, 75, 76, 92
transition, 112
uniform, 101
vector, 115
weight, 93
sensitivity, 92
sequence model
Bernoulli, 12
Markov chain, 12
similar sequence alignment, 57
Smith-Waterman algorithm, 10, 61, 71
sorting, 22
space-saving strategy, 50
spaced seed, 75, 76, 92
specificity, 92
suboptimal alignment, 58
substitution, 3
matrix, 8
suffix array, 67
suffix tree, 66
sum-of-pairs, 11, 83
tabular computation, 24
target frequency, 134
transition, 112
seed, 112
transversion, 112
UCSC Genome Browser, 78, 87
ungapped BLAST, 69
vector seed, 115
Wu-BLAST, 143
YAMA, 87