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336 | Index
sequences (continued)
transcripts for proteins, 36
xdget, 184
serial searches
accurate alignment, 152
BLAST and, 222–224
BLASTX and, 149
long sequences, 153
undocumented genes, 157
serine (S), 24
setdb (WU-BLAST), 168, 180
SGD database, 204
SGE distributed resource management, 219
Shannon, Claude, 56
Shannon’s Entropy, 56
shotgun sequence, 141, 149, 151
silent mutations, 28
SIM4 program, 135
similarity
biological sequences and, 38
patterns of, 27
vectors, 142
weak, 117
simple repeats, 37
Smith-Waterman algorithm
alignment endpoints, 81
BLAST statistics compared, 102
blastpgp parameter, 263
gold standard, 76
(see also local alignment)
soft masking
BLASTP searches, 145
case sensitivity and, 133
cross-species exploration, 135
functionality, 120
low-complexity and, 150
seeding and, 81, 233
sensitive searches, 146
software
optimization, 220–224
sequence management, 211, 212
source code (NCBI-BLAST), 161, 224
source, message and symbols from, 56
SOURCE (sequence record), 203
sp2fasta (WU-BLAST file), 168
span parameter (WU-BLAST), 279
span1 parameter (WU-BLAST), 279
span2 parameter (WU-BLAST), 279
species, 134
specificity, 131, 133, 147
SPIDEY program, 135
splicing
alternative, 157
coding sequences and, 36
regulation and, 138
transcript clustering, 140
SRS (Sequence Retrieval System), 211
stacking, 139
start codons, 26
statistics
massaging, 128, 129
redundant sequences and, 196
statistical outliers, 128
(see also specific methods)
Stein, Lincoln, 305
stop codons
alignment and, 124, 158, 184
BLASTX, 149
defined, 26
mutation and, 28
preventing, 155
prokaryotic genes, 36
pseudogenes, 38, 124, 153
TBLASTX search, 175
storage considerations, 207
strandedness
BLAST, 92
BLASTX, 93
TBLASTX, 93
sts database, 197
Stuffit Expander, 166
substitution matrix (see scoring matrix)
substitution, nonconservative, 28
sum score
alignments and, 102
calculating, 106
Expect and, 103, 104
overview, 67–70, 104
sumScore function, 106
suppressors, 36
SWISS-PROT database, 197, 204
symbolic links, 163
symbols, message and, 56
synonymous mutations, 28
synteny, 136
T
T= parameter (WU-BLAST), 280
tabular format
blast-imager.pl, 305
BLASTN and, 133
converting to, 118, 309
megablast and, 172

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