BLAST

This is the Title of the Book, eMatter Edition

Copyright © 2012 O’Reilly & Associates, Inc. All rights reserved.

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