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Index | 333
postsw parameter (WU-BLAST), 278
precision, 59, 284
pressdb (WU-BLAST), 168, 180, 184
1˚ (primary) structure, 25
priming, 132, 138, 140
probability
defined, 55
overview, 56
P-value and, 70
sum, 69
prokaryotes, 33, 35
proline (P), 24
ProPBS DRM, 219
PROSITE format, 257, 261
protein sequence
BLAST and, 75, 197
blastclust, 264
cDNAs and, 123
example, 24, 26, 291
GenBank, 4
INSD, 199
mutation and, 28, 32
PAM matrices, 60
PSI-BLAST, 237
translating to, 25, 27
WU-BLAST, 180, 271
proteins
average length, 36, 67
BLASTP searches, 144, 172, 181
BLASTX searches, 147, 151
BLOSUM matrices and, 60
coding sequence for, 36
est database, 197
ESTs and, 137, 149
fastacmd parameter, 244
formatdb parameter, 241
genes and, 22
hypothetical, 123
low-complexity sequence, 120
mapping to genomes, 152, 154
mining ESTs, 154, 155
mutation and, 28
natural selection and, 30
nr database and, 197
overview, 22–25
percent identity and, 148
PHI-BLAST, 178
PSI-BLAST, 176
public repository, 199
redundant, 197
RNA polymerase, 22
sequencing transcripts for, 36
TBLASTN searches, 154, 174
protista, 33
protocols (BLASTN), 131–144
pseudogenes
BLASTX, 149
conservation, 138
cross-species exploration, 136
mapping DNA/EST to genomes, 135
overview, 38
stop codons, 124, 153
PSI-(pattern-hit initiated) BLAST
BLAST program, 76
blastpgp parameters, 256–257
checkpoint file, 237
composition-based lambda, 62
display formats, 291–298
features, 176–178
reference, 257
sensitive searches, 147
psitblastn (blastall), 236, 237
PSSM (position-specific scoring matrix)
blastgpg parameter, 263
blastpgp parameter, 259, 260
PSI-BLAST, 236, 256
public domain (NCBI-BLAST), 161, 224
PubMed, 4
purine (R), 21, 26
P-value
alignment groups, 94
BLASTP, 91
converting raw scores, 97
HSPs and, 69
search space and, 84
WU-BLAST and, 70, 102
pyrimidine (Y), 21, 26
Q
Q= parameter (WU-BLAST), 278
qoffset= parameter (WU-BLAST), 278
qrecmax= parameter (WU-BLAST), 278
Qrecmin= parameter (WU-BLAST), 278
queries
BLASTN search, 4–12
databases and, 206, 208
long-running, 120
query chopping, 221
query packing
defined, 220, 221
oligos and, 132
vector clipping, 142

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