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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
restest parameter (WU-BLAST), 279
results
choosing format, 7, 8
viewing, 8–12
retro-pseudogenes, 38
retrotransposons, 37
retroviruses, 37
reverse transcriptase, 36
ribosomal RNA (rRNA), 22, 37
ribosomes, 25
RID (Request Identifier), 8
RNA
noncoding RNA, 22, 25, 37
ribosomal RNA, 22, 37
transcription, 22
transfer RNA, 22, 37
viruses and, 35
(see also mRNA)
RNA polymerase, 22
rounding errors, 61, 108
rpsblast (NCBI-BLAST), 162, 256
rRNA (ribosomal RNA), 22, 37
S
S= parameter (WU-BLAST), 279
Saccharomyces cereviseae, 33
Saccharomyces Genome Database, 199
same-sense mutations, 28
saturated sequences, 31, 32
scaling factors, 61
scientific experiments
controls and, 117
designing, 119
pilots and, 128
searches as, 116

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