July 2003
Intermediate to advanced
368 pages
13h 44m
English
Content preview from BLAST
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Index | 329
overview, 65–67
parameters/values for, 98
keratin (protein), 22
KEYWORDS (sequence record), 203
Kimura, Motoo, 31
L
λ (lambda)
defined, 61, 62
example, 63
Expect, 101
expected HSP length, 112
footer, 11
gapped alignments, 66
gaps and, 86
nat scores and, 100
raw scores and, 111
report differences, 113
scoring schemes and, 111
sequence similarity, 64
ungapped values, 187
WU-BLAST parameter, 272, 275
L= parameter (WU-BLAST), 275
L2 cache, 215
lcfilter parameter (WU-BLAST), 275
lcmask parameter (WU-BLAST), 275
leucine (L), 22, 28, 58
licensing, 167, 268
Linkout option (report), 9
links parameter (WU-BLAST), 128, 275
LION Biosciences, 211
local alignment
defined, 40
global versus, 50
Karlin-Altschul statistics, 65
mapping DNA/EST to genomes, 134
overview, 46–50
reduced memory and, 51, 52
TBLASTX searches and, 157
theories and, 55
transcripts and genomic structure, 53
locus identifier, 5, 203, 242
LocusLink, 4, 9
lod scores
defined, 58
example, 58
normalized scores and, 61
precision and, 59
target frequencies and, 60
low-complexity sequence
BLAST searches, 81
blastall parameter, 232
BLASTX searches, 148
chance occurrences, 120
cross-species exploration, 136
genomes, 121
mapping genomes, 131, 133, 135
raw sequencing reads, 142
repeat masking, 143
sensitive searches, 146
simple repeats and, 37
TBLASTX searches, 156
transcript ...
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I'm always learning. So when I got on to O'Reilly, I was like a kid in a candy store. There are playlists. There are answers. There's on-demand training. It's worth its weight in gold, in terms of what it allows me to do.