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BLAST by Joseph Bedell, Mark Yandell, Ian Korf

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This is the Title of the Book, eMatter Edition
Copyright © 2012 O’Reilly & Associates, Inc. All rights reserved.
Index | 325
mapping DNA/EST to genomes, 135
repeat proximity, 138
WU-BLASTN defaults, 113
Expect
BLAST statistics, 102
BLASTP, 91
calculating, 99
footer reports, 88
frame/size corrected, 108
grouping and, 107
of HSP, 101
pair-wise sum P-value, 106, 108
raw scores, 97, 104
sum score, 103, 104, 106
expectation value
bl2seq parameter, 253
blastall, 232
blastpgp parameter, 259
megablast, 247
expected HSP length
BLASTX query and, 105
calculating Expect, 99
Karlin-Altschul statistics, 66
lambda and, 112
search space and, 67
expected score, 62, 63, 65
expectedHSPlength function, 112, 113
exploring
BLAST experiments, 130
BLASTP searches, 131, 144
BLASTX searches, 147
cross-species sequence, 135, 136
ESTs/genomic DNA, 137–139
expressed sequence tags (see ESTs)
expression, genes and, 137, 157
eXtensible Markup Language (XML),
12, 295
extension
bl2seq parameter, 255
blastall parameter, 239
BLASTX search, 151
exons and, 148
sequencing errors and, 155
transcripts and, 139, 140
extension phase, 120
F
FASTA files
accession numbers, 208
annotating ESTs, 149
blastclust, 265
BLASTP, 90
fastacmd, 176, 243
flat file indexing, 209
formatdb, 240, 242
formatting and, 208
multiple sequences, 150
overview, 188–192
plus strand, 91
shuffling, 117
splitting, 122
xdget, 287
FASTA format
BLASTX, 93
GI numbers, 222
queries and, 5
reporting data, 207
sequence databases, 199
xdformat, 284
fastacmd
FASTA files, 208
features, 175, 176
installation files, 162
parameters, 242–245
retrieving sequences, 191
virtual databases, 194
FEATURES (sequence record), 203
field programmable gate array (FPGA), 225
FileMaker, 210
files
large databases, 193
NCBI-BLAST installation, 162
WU-BLAST installation, 167
fill phase, 42–44, 52
filter= parameter (WU-BLAST), 271
filtering
blast2table.pl, 309
blastall parameter, 232
blastpgp parameter, 260
megablast parameter, 247, 251
query sequence, 271, 275
WU-BLAST parameter, 271
(see also complexity filters)
final threshold, 86
fixed alleles, 31
flat files, 199–204, 209–211
FlyBase database, 199, 204
footer reports, 11, 88, 99, 119
formatdb
alias databases, 195
BLAST databases, 193
FASTA files, 208
features, 171
installation files, 162

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