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Index
Numbers
3-prime (3´), 20, 132
5-prime (5´), 20
Synbols
* (asterisk), 149, 184
[] (brackets), 192, 257
: (colon), 169, 244
- (dash)
NCBI display formats, 292, 294
NCBI-BLAST, 229
PHI-BLAST, 257
PSI-BLAST, 258
Unix and, 194
xdformat and xdget, 269
. (dot), 14, 292
> (greater than sign), 5, 188
() parentheses, 203
| (pipe), 5, 189, 193, 292
+ (plus), 292
" (quotes), 231
A
Abstract Syntax Notation One (see ASN.1)
Accelrys package, 211
accession number
blastn and, 181
FASTA files and, 208
fastacmd parameter, 243, 244
formatdb parameter, 242
megablast parameter, 247
NCBI identifier, 5
one-to-one mapping, 207
public databases and, 189
sequence records and, 172, 202, 203
xdformat parameter, 282
xdget parameter, 286
actual length, 99, 105
adenine (A), 20, 22
affine gaps
blastall parameter, 236
defined, 51
megablast parameter, 246, 247, 249
AG-BLAST, 224, 225
α-helix, 25
alanine (A), 22
algorithms
alignment, 51, 64, 152
big-O notation, 50
BLAST, 76–87
BLAT, 152
HMMER, 147
(see also two-hit algorithm)
alias databases
features, 195
formatdb and, 193, 196, 240, 241
GI numbers and, 222
WU/NCBI-BLAST differences, 268
alignment
algorithms, 51, 64, 152
alternate views, 13
BLAST reporting, 88, 90–95
blastall parameter, 232
blastpgp parameter, 258
cross-species exploration, 135
defined, 76
This is the Title of the Book, eMatter Edition
Copyright © 2012 O’Reilly & Associates, Inc. All rights reserved.
320 | Index
alignment (continued)
determining significance, 111
ESTs and, 138
gaps and, 65
insensitive search, 146
mapping and, 130
number expected by chance, 119
overcalling and, 142
percent identity and, 148
query chopping and, 221
repeats and, 143
score metric, 55
search space and, 65
stop codons, 124, 158, 184
sum score, 102
TBLASTN, 93
TBLASTX, 93
vectors, 142
alignment groups
BLAST report, 94
exons and, 148
links and topcomboN, 128
WU-BLAST, 128
alignment threshold, 84, 120
Alignments option (report), 9
allele frequencies, 30
alleles, 29, 31
Altivec, 224
Altschul, Stephen, 65
altscore parameter (WU-BLAST), 187, 269
amino acid similarity, 57–59, 64
amino acids (aa)
databases, 197
difficulty sequencing, 123
genetic code, 25
PHI-BLAST and, 257
proteins and, 22, 25
PSI-BLAST and, 176
scoring matrices, 60
symbols listed, 22–24
annealing, 131
annotating
concatenating lines and, 150
ESTs, 149, 151
Apple Computer, 224
Archaea, 33
arginine (R), 24, 58
ASCII format, 262
ASN.1 (Abstract Syntax Notation One)
bl2seq parameter, 252
format, 296, 298
formatdb parameter, 240
reports and, 12
asparagine (N), 24
aspartate (D), 22
asterisk (*), 149, 184
ATG (start codon), 26
B
B= parameter (WU-BLAST), 270
Bacteria, 33
bandwidth, 52
base pair (bp), 21, 126, 134
Basic Local Alignment Search Tool
(see BLAST)
batch retrieval systems, 198
benchmarking
blastn, 215
blastp, 172, 182, 215
EST search, 181
systems, 215
Beowulf clusters, 217
big-O notation, 50
biological sequences, 35–38, 64
(see also evolution; genes; genomes;
molecular biology)
Bioperl
annotating ESTs, 151
clustering and, 141
database purifiers, 196
parsing, 126–127
repeat masking and, 143
bit score
defined, 100
Expect and, 101, 103
lambda and, 111
bitScoreToExpect function, 102
bl2seq (NCBI-BLAST)
BLASTX and, 152, 158
exons and, 126, 134, 152
functionality, 175
HSPs and, 153, 155
installation files, 162
parameter, 252–255
BLAST algorithm
evaluation, 84–87
extension, 81–84
overview, 76, 77
seeding, 77–81
BLAST (Basic Local Alignment Search Tool)
custom databases, 198
functionality, 3
implementation, 79
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Copyright © 2012 O’Reilly & Associates, Inc. All rights reserved.
Index | 321
optimizing, 213
report formats, 88–95
search tips, 116–129
serial searching, 222–224
standard databases, 197
statistical outliers, 128
traditional programs, 75
viewing graphically, 118
blast2table.pl, 309
blasta (WU-BLAST), 168, 169
blastall (NCBI-BLAST)
error messages, 180
installation files, 162
parameters, 230–240
blastclust (NCBI-BLAST)
clustering with, 141
installation files, 163
parameters, 264–266
BLASTDB environment variable, 163, 164,
169
BLASTFILTER environment variable, 169
blast.hqx (OS 9), 166
blast-imager.pl, 305
BlastMachine, 225
BLASTMAT environment variable,
164, 169, 187
BLASTN
alignment format, 93
benchmarking speed, 215
BLAST program, 75
display formats, 291–298
ESTs and, 171
implementation, 79, 83, 87
I/O considerations, 220
Karlin-Altschul statistics, 109–114
reporting format, 91–93
searches, 4–12, 130, 131–144
seeding, 224
strandedness, 92
as WU-BLAST component, 181
as NCBI-BLAST component, 172
BLASTP
alignments, 90–91
benchmarking, 172, 182, 215
BLAST program, 75
composition-based lambda, 62
display formats, 291–298
implementation considerations, 79, 83
sample HSP, 97
searches, 144–147, 172, 181
strandedness, 92
blastpgp (NCBI-BLAST)
installation files, 162
parameters, 256–264
PHI-BLAST, 176, 178
BLASTX
alignment, 93
BLAST program, 75
display formats, 291–298
effective length, 105
gene-finding tool, 173, 182
searches, 147–152, 223
strandedness, 92
sum scores and, 68
translations, 108
ungapped alignment, 124
BLASTZ, 76, 164
BLAT algorithm, 152
blocks, 60
BLOSUM (BLOcks SUbstitution)
BLASTX searches, 148
insensitive search and, 146
overview, 60
relative entropy, 62
book of life, 19, 55
bottom parameter (WU-BLAST), 270
Boutell, Thomas, 305
bp (base pair), 21, 126, 134
brackets [], 192, 257
β-sheet, 25
bus speed, 215
C
caching
database splitting and, 222
files, 213–215
pipelines and, 214, 215
carcinogens, 28
case sensitivity
bl2seq parameter, 255
BLAST reports, 93
databases and, 133, 208
fastacmd, 242
genomic DNA and, 148
megablast parameter, 251
true/false switches, 229
WU-BLAST parameter, 275
cDNA (complementary DNA)
ESTs and, 123, 137
mapping to genomes, 134, 135
protein sequences and, 123
reverse transcriptase and, 36
cDNA library, 36, 138

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