Bioinformatics and Functional Genomics, Second Edition

Subject Index

AAT program, 666

ABCD1 gene, 734, 857

Aberrations, chromosomal, 683, 863

Ab initio approaches:

bacterial and archaeal genomes, 618

gene-finding software, 666, 755

genome analysis, 782

prediction of protein structure, 450–451, 455

Absolute value, 346

Accepted point mutations, 58–63, 217. See also PAM matrices

Accession numbers, significance of, 27–28, 33, 37, 51–52, 90, 106, 128, 196, 198, 248

Accuracy, in microarray data analysis, 344–345

Acetylcholine, 768

Acetyltransferases, 39

ACOR, 883

Acrylamide gel, 382–383, 544

Actin, 224, 817

Actinobacteria, 600

Actinomycetes, 603

Acyl-CoA dehydrogenases, 718

Acyrthosiphon pisum, 609

ADAM 20, 653

Adaptation, 216

ADE2, 468

Adenine, 64, 110, 242, 286, 545

Adenoma, 874

Adenosine:

cyclic (cAMP), 398, 756

monophosphate (AMP), 127

triphosphate (ATP), 408, 545–546, 732, 858

Adenovirus, 570

Adenylate kinase, 223

Adhesin, 579

Adhesion molecules, 397, 579, 758

ADP, 224

Adrenoleukodystrophy, 718, 848, 850

Advanced database searching:

characteristics of, 141–142

hidden Markov models (HMM), 152, 156–161, 174

gene discovery using BLAST, 169–173

pitfalls of, 174

position-specific iterated BLAST (PSI-BLAST), 145–156, 174

PSSM, 146–153, 174

rapid search of genomic DNA, 161–169

SAM, 174

specialized BLAST sites, 142–145

web resources, 175

Aedes spp., 762, 764

Aeropyrum pernix, 533, 601, 608

Affinity chromatography, 499–500

Affymetrix, 315–317, 332, 333–335, 337, 343, 345–346

Affymetrix GeneChip, 343

Agarose gel, 293

Agglomerative hierarchical ...