July 2003
Intermediate to advanced
368 pages
13h 44m
English
Content preview from BLAST
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324 | Index
effectiveLengthSeq function, 106, 114
EMBL (European Molecular Biology
Laboratory)
accession numbers, 189
est database, 197
flat files, 199, 201
INSD, 198
locus, 203
nucleotide sequences, 5
organism names, 203
version number, 203
enhancers, 36
entropy
conservation and, 138
defined, 56
example, 57
(see also relative entropy)
environment variables
BLASTDB, 163, 164, 169
BLASTFILTER, 169
BLASTMAT, 164, 169, 187
NCBI-BLAST, 163, 179
PATH, 163, 164
WU-BLAST, 169, 186
enzymes, 21, 36, 178, 188
errors parameter (WU-BLAST), 271
Escherichia coli, 33, 197
est database, 197
EST2GENOME program, 135
ESTs (expressed sequence tags)
alignment, 138
annotating, 137–139, 149, 151
BLASTN search, 171, 181
CDNA library, 138
clustering, 141
contaminants in databases, 123
defined, 37
EST2GENOME, 135
fastacmd program, 175
gaps in coverage, 126
mapping to genomes, 134, 135
mining, 154, 155
proteins and, 149
raw sequencing and, 124
TBLASTN searches, 174, 183
TBLASTX searches, 157
transcript clustering, 140
transcripts, 197
unannotated proteins and, 154
xdformat, 180
⁄etc⁄sysblast file, 169, 170
euchromatic (nonrepetitive DNA)
sequence, 110
eukaryotes
gene structure, 36
genome division, 33
genomic structure, 35, 53
nucleus and, 33
pseudogenes in, 38
repetitive elements, 143
viruses and, 35
Eurcarya, 33
E-value
alignment and, 84, 86, 94, 119
annotating ...
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O’Reilly covers everything we've got, with content to help us build a world-class technology community, upgrade the capabilities and competencies of our teams, and improve overall team performance as well as their engagement.Julian F.
I wanted to learn C and C++, but it didn't click for me until I picked up an O'Reilly book. When I went on the O’Reilly platform, I was astonished to find all the books there, plus live events and sandboxes so you could play around with the technology.Addison B.
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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.