BLAST

This is the Title of the Book, eMatter Edition

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

Index | 333

postsw parameter (WU-BLAST), 278

precision, 59, 284

pressdb (WU-BLAST), 168, 180, 184

1˚ (primary) structure, 25

priming, 132, 138, 140

probability

defined, 55

overview, 56

P-value and, 70

sum, 69

prokaryotes, 33, 35

proline (P), 24

ProPBS DRM, 219

PROSITE format, 257, 261

protein sequence

BLAST and, 75, 197

blastclust, 264

cDNAs and, 123

example, 24, 26, 291

GenBank, 4

INSD, 199

mutation and, 28, 32

PAM matrices, 60

PSI-BLAST, 237

translating to, 25, 27

WU-BLAST, 180, 271

proteins

average length, 36, 67

BLASTP searches, 144, 172, 181

BLASTX searches, 147, 151

BLOSUM matrices and, 60

coding sequence for, 36

est database, 197

ESTs and, 137, 149

fastacmd parameter, 244

formatdb parameter, 241

genes and, 22

hypothetical, 123

low-complexity sequence, 120

mapping to genomes, 152, 154

mining ESTs, 154, 155

mutation and, 28

natural selection and, 30

nr database and, 197

overview, 22–25

percent identity and, 148

PHI-BLAST, 178

PSI-BLAST, 176

public repository, 199

redundant, 197

RNA polymerase, 22

sequencing transcripts for, 36

TBLASTN searches, 154, 174

protista, 33

protocols (BLASTN), 131–144

pseudogenes

BLASTX, 149

conservation, 138

cross-species exploration, 136

mapping DNA/EST to genomes, 135

overview, 38

stop codons, 124, 153

PSI-(pattern-hit initiated) BLAST

BLAST program, 76

blastpgp parameters, 256–257

checkpoint file, 237

composition-based lambda, 62

display formats, 291–298

features, 176–178

reference, 257

sensitive searches, 147

psitblastn (blastall), 236, 237

PSSM (position-specific scoring matrix)

blastgpg parameter, 263

blastpgp parameter, 259, 260

PSI-BLAST, 236, 256

public domain (NCBI-BLAST), 161, 224

PubMed, 4

purine (R), 21, 26

P-value

alignment groups, 94

BLASTP, 91

converting raw scores, 97

HSPs and, 69

search space and, 84

WU-BLAST and, 70, 102

pyrimidine (Y), 21, 26

Q

Q= parameter (WU-BLAST), 278

qoffset= parameter (WU-BLAST), 278

qrecmax= parameter (WU-BLAST), 278

Qrecmin= parameter (WU-BLAST), 278

queries

BLASTN search, 4–12

databases and, 206, 208

long-running, 120

query chopping, 221

query packing

defined, 220, 221

oligos and, 132

vector clipping, 142