July 2003
Intermediate to advanced
368 pages
13h 44m
English
Content preview from BLAST
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This is the Title of the Book, eMatter Edition
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334 | Index
query sequence
BLASTN, 91
BLASTP, 91
blastpgp parameter, 260
BLASTX, 93
effective length, 105
example, 5, 9
filtering, 120, 263, 271, 275
megablast parameter, 247, 248
quotes ("), 231
R
R= parameter (WU-BLAST), 279
random coil, 25
raw score
converting, 97
converting to normalized score, 64
defined, 59, 100
Expect and, 104
expected score, 62
HSPs and, 104
Karlin-Altschul, 101
lambda and, 61, 111
ungapped alignments, 113
rawScoreToBitScore function, 102
rawScoreToExpect function, 102
reading frame
BLASTP, 91
BLASTX format, 93
overlapping, 108
translating DNA, 27
(see also ORF)
reclustering, 266
redundancy, 185, 196, 197
RefSeq
features, 204
GenBank and, 197
NCBI toolbox, 4
nucleotide sequences, 5
regulation, splicing and, 138
relative entropy, 62, 67
RepeatMasker, 143
repeats
alignments and, 133
dinucleotide, 37
genomic DNA and, 121, 137, 148, 156
genomic sequences and, 153
long-running queries and, 120
mapping DNA/EST to genomes, 135
masking, 143
overlapping, 138, 150
overview, 37
RepeatMasker, 143
transcript clustering, 140
repetitive elements
contamination and, 144
duplication and, 38
eurkaryotic genomes, 143
exons and, 138
false associations, 141
FEATURES and, 203
genes and, 135
genomes and, 121
reports
BLAST structure, 88
footer, 11, 88, 99, 119
formats, 88–95
formatting considerations, 208
Request Identifier (RID), 8
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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.
I’ve been on the O’Reilly platform for more than eight years. I use a couple of learning platforms, but I'm on O'Reilly more than anybody else. When you're there, you start learning. I'm never disappointed.Amir M.
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.