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Index | 327
repeats and, 37, 121
sequencing projects, 37
shotgun coverage, 124
simple repeats, 37
TBLASTX searches, 155, 157, 174, 183
viruses, 35
genomic DNA
annotating with ESTs, 137–139
BLASTX searches, 148
contaminants and, 197
finding correct structure, 123
finding undocumented genes, 156–157
gene finding in, 147–149
masking repeats, 121, 137, 148, 156
memory and, 51
genomic sequence
aligning transcripts, 53
alignment, 50
BLASTX searches, 173, 182
htg database, 198
identifying genes in, 137–139
mapping, 151
poly-A tail, 153
repeats and, 153
segment large, 121, 122
serial searching, 222
shotgun reads, 150, 154
TBLASTX, 93
GI (GenInfo Identifier) number
alias databases, 222
blastall parameter, 234
compound identifiers, 191
example, 5
fastacmd parameter, 244
formatdb parameter, 196, 241
GILIST and, 195
indexes and, 203
megablast parameter, 247, 248
VERSION field and, 201
WU-BLAST parameter, 273
gi parameter (WU-BLAST), 273
GIF format, 118, 305
GILIST (alias databases), 195
Gish, Warren, 267
global alignment
file phase, 42–44
initialization phase, 42
local versus, 50
overview, 40–41
reduced memory and, 51, 52
trace-back, 44–46
transcripts and genomic sequences, 53
glutamate (E), 22
glutamine (Q), 24
glycine (G), 22
golf= parameter (WU-BLAST), 273
golmax= parameter (WU-BLAST), 273
greater than sign (>), 5, 188
gspmax= parameter (WU-BLAST), 273
gss (genome survey sequences), 197
gt2fasta (WU-BLAST file), 168
guanine (G), 20, 22
H
H= parameter (WU-BLAST), 274
H (relative entropy of scoring matrix)
BLASTP searches, 145
defined, 62
footer, 11
gapped alignments, 66
match-mismatch scoring, 62
ungapped values, 187
hardware optimization, 213–220
HI (hit initiation) tag (PHI-BLAST), 257
high-scoring pair (see HSP)
histidine (H), 22
Hit Table alignment view, 13
hitdist= parameter (WU-BLAST), 146, 274
hits
blastpgp parameter, 261
defined, 90
mapping oligo/genomes, 132
megablast parameter, 250
multiple HSPs as, 102
troubleshooting, 119
WU-BLAST parameter, 270
HMMER algorithm, 147
homology
cross-species exploration, 136
proteins and, 152
PSI-BLAST, 176
sequences, 32
horizontal gap score, 42, 43
HSP (high-scoring pair)
BLAST and, 76
BLASTP search, 97
exons and, 134, 139
Expect of, 62, 101
final threshold, 84
frame-shifts, 149, 153
junk and, 138
megablast parameter, 248
normalized scores, 67
pair-wise sum P-value, 107

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