Concise Encyclopaedia of Bioinformatics and Computational Biology (eBook)

John M. Hancock, Marketa J. Zvelebil (Herausgeber)

eBook Download: EPUB

2014 | 2. Auflage
John Wiley & Sons (Verlag)
978-1-118-59815-3 (ISBN)

Infos

Concise Encyclopaedia of Bioinformatics and Computational Biology, 2nd Edition is a fully revised and updated version of this acclaimed resource. The book provides definitions and often explanations of over 1000 words, phrases and concepts relating to this fast-moving and exciting field, offering a convenient, one-stop summary of the core knowledge in the area. This second edition is an invaluable resource for students, researchers and academics.

Autor

John M. Hancock: Group Leader in Bioinformatics, Functional Genomics Team, MRC Harwell. Marketa Zvelebil: Group Leader: Cancer Informatics Unit, Breakthrough Cancer Research, Institute of Cancer Research, London.

Inhalt

Title Page 2
Copyright 3
Dedication 5
List of Contributors 6
Preface 12
A 14
Ab Initio 17
Further reading 17
Ab Initio Gene Prediction, see Gene Prediction, ab initio. 18
ABNR, see Energy Minimization. 19
Accuracy (of Protein Structure Prediction) 20
Accuracy Measures, see Error Measures. 21
Adjacent Group 22
Further reading 22
Admixture Mapping (Mapping by Admixture Linkage Disequilibrium) 23
Further reading 23
Adopted-basis Newton–Raphson Minimization (ABNR), see Energy Minimization 25
Affine Gap Penalty, see Gap Penalty. 26
Affinity Propagation-based Clustering 27
Further reading 28
Affymetrix GeneChip™ Oligonucleotide Microarray 29
Further reading 30
Affymetrix Probe Level Analysis 31
Further reading 32
After Sphere, see After State. 34
After State (After Sphere) 35
Further reading 35
AIC, see Akaike Information Criterion. 36
Akaike Information Criterion 37
Further reading 37
Algorithm 39
Alignment (Domain Alignment, Repeats Alignment) 40
Further reading 43
Alignment Score 45
Further reading 45
Allele-Sharing Methods (Non-parametric Linkage Analysis) 46
Further reading 47
Allelic Association 49
Further reading 50
Allen Brain Atlas 51
Further reading 51
Allopatric Evolution (Allopatric Speciation) 52
Further reading 52
Allopatric Speciation, see Allopatric Evolution. 53
AlogP 54
Alpha carbon, see C? (C-Alpha). 55
Alpha Helix 56
Further reading 56
Alternative Splicing 57
Further reading 58
Alternative Splicing Gene Prediction, see Gene Prediction, alternative splicing. 59
Amide Bond (Peptide Bond) 60
Further reading 60
Amino Acid (Residue) 61
Amino Acid Abbreviations, see IUPAC-IUB Codes. 63
Amino Acid Composition 64
Amino Acid Exchange Matrix (Dayhoff Matrix, Log Odds Score, PAM (Matrix), BLOSUM Matrix) 65
Further reading 66
AMINO Acid Substitution Matrix, see Amino Acid Exchange Matrix. 68
Amino-terminus, see N-terminus. 69
Amphipathic 70
Further reading 70
Analog (Analogue) 71
Further reading 71
Ancestral Lineage, see Offspring Lineage. 72
Ancestral State Reconstruction 73
Software 73
Further reading 74
Anchor Points 75
Annotation Refinement Pipelines, see Gene Prediction. 76
Annotation Transfer (Guilt by Association Annotation) 77
Further reading 77
APBIONET (Asia-Pacific Bioinformatics Network) 78
Apomorphy 80
Further reading 80
APOLLO, see Gene Annotation, visualization tools. 82
Arc, see Branch (of a Phylogenetic Tree). 83
Are We There Yet?, see AWTY. 84
Aromatic 85
Further reading 85
Array, see Data Structure. 87
Artificial Neural Networks, see Neural Networks. 88
ASBCB (The African Society for Bioinformatics and Computational Biology) 89
Association Analysis (Linkage Disequilibrium Analysis) 90
Further reading 91
Association Rule, see Association Rule Mining. 93
Association Rule Mining (Frequent Itemset, Association Rule, Support, Confidence, Correlation Analysis) 94
Further reading 96
Associative Array, see Data Structure. 97
Asymmetric Unit 98
Atomic Coordinate File (PDB file) 99
Autapomorphy 100
Further reading 100
Autozygosity, see Homozygosity, Homozygosity Mapping. 102
AWTY (Are We There Yet?) 103
Further reading 103
Axiom 104
B 105
Backbone (Main Chain) 108
Further reading 108
Backbone Models 109
Further reading 109
Backpropagation Networks, see Neural Networks. 111
Bagging 112
Further reading 112
Ball and Stick Models 113
Further reading 114
BAMBE (Bayesian Analysis in Molecular Biology and Evolution) 115
Further reading 115
Base-Call Confidence Values 117
Base Composition (GC Richness, GC Composition) 118
Further reading 118
Bayes' Theorem 119
Further reading 119
Bayesian Classifier (Naïve Bayes) 120
Further reading 121
Bayesian Evolutionary Analysis Utility, see BEAUti. 122
Bayesian Information Criterion (BIC) 123
Further reading 123
Bayesian Network (Belief Network, Probabilistic Network, Causal Network, Knowledge Map) 125
Further reading 126
Bayesian Phylogenetic Analysis 127
Software 127
Further reading 128
BEAGLE 129
Further reading 129
Beam Search 130
Further reading 130
BEAST (Bayesian Evolutionary Analysis by Sampling Trees) 131
Further reading 131
BEAUTI (Bayesian Evolutionary Analysis Utility) 132
Before State (Before Sphere) 133
Further reading 133
Belief Network, see Bayesian Network. 134
Bemis and Murcko Framework (Murcko Framework) 135
Further reading 135
Best-First Search 136
Further reading 136
Beta Barrel 137
Further reading 137
Beta Breaker 138
Further reading 138
Beta Sheet 139
Further reading 139
Beta Strand 140
Further reading 140
BIC, see Bayesian Information Criterion. 141
Biclustering Methods 142
Further reading 142
Bifurcation (in a Phylogenetic Tree) 144
Binary Numerals 145
Binary Relation 146
Binary Tree, see Data Structure. 147
Binding Affinity (Kd, Ki, IC50) 148
Binding Site 149
Further reading 149
Binding Site Symmetry 150
Bio++ 154
Bioactivity Database 155
Bioinformatics (Computational Biology) 157
The Bioinformatics Organization, Inc (formerly bioinformatics.org) 159
Bioinformatics Training Network, see BTN. 160
Biological Identifiers 161
BioMart 162
Further reading 162
Bipartition, see Split 163
Bit 164
Further reading 165
BLAST (Maximal Segment Pair, MSP) 166
Further reading 169
BLASTX 170
Further reading 170
BLAT (BLAST-like Alignment Tool) 171
Further reading 171
BLOSUM (BLOSUM Matrix) 172
Further reading 173
Boltzmann Factor 174
Further reading 174
Boolean Logic 175
Boosting 176
Further reading 176
Bootstrap Analysis, see Bootstrapping. 178
Bootstrapping (Bootstrap Analysis) 179
Software 180
Further reading 181
Bottleneck, see Population Bottleneck. 182
Box 183
Further reading 183
Branch (of a Phylogenetic Tree) (Edge, Arc) 184
Branch Length, see Branch, Branch-length Estimation. 185
Branch-length Estimation 186
Software 186
Further reading 187
BTN (Bioinformatics Training Network) 188
C 189
C-? (C-alpha) 194
Further reading 194
Cancer Gene Census (CGC) 195
Further reading 195
Candidate Gene (Candidate Gene-based Analysis) 196
Further reading 197
Carboxy-Terminus, see C-Terminus. 198
CASP 199
Further reading 200
Catalogue of Somatic Mutations in Cancer, see COSMIC 201
Catalytic Triad 202
Further reading 202
Category 204
Causal Network, see Bayesian Network 205
CCDS (Consensus Coding Sequence Database) 206
Further reading 206
CDS, see Coding Region. 207
Centimorgan 208
Further reading 208
Centromere (Primary Constriction) 209
Further reading 209
CGC, see Cancer Gene Census. 211
Channel Capacity (Channel Capacity Theorem) 212
Further reading 212
Character (Site) 213
Further reading 213
CHARMM 214
Further reading 214
Chemical Biology 215
Chemical Hashed Fingerprint 216
Chemoinformatics 217
ChIP-seq 218
Further reading 219
Chou & Fasman Prediction Method
Further reading 220
Chromatin 221
Further reading 221
Chromosomal Deletion 222
Further reading 222
Chromosomal Inversion 223
Further reading 223
Chromosomal Translocation 224
Further reading 224
Chromosome 225
Further reading 225
Chromosome Band 226
Further reading 226
Circos, see Gene Annotation, visualization tools. 228
Cis-regulatory Element 229
Cis-regulatory Module (CRM) 230
Cis-regulatory Module Prediction 232
Further reading 232
Clade (Monophyletic Group) 234
Further reading 234
Cladistics 235
Further reading 235
Clan 236
Further reading 236
Classification 237
Classification in Machine Learning (Discriminant Analysis) 238
Further reading 238
Classifier (Reasoner) 239
Classifiers, Comparison 240
Further reading 240
ClogP 242
CLUSTAL 243
Further reading 244
Clustal Omega, see Clustal. 246
ClustalW, see Clustal 247
ClustalX, see Clustal. 248
Cluster 249
Further reading 249
Cluster Analysis, see Clustering. 250
Cluster of Orthologous Groups (COG, COGnitor) 251
Further reading 252
Clustering (Cluster Analysis) 253
Clustering Analysis, see Clustering. 255
CNS 256
Further reading 256
Code, Coding, see Coding Theory. 257
Coding Region (CDS) 258
Further reading 258
Coding Region Prediction 259
Coding Statistics (Coding Measure, Coding Potential, Search by Content) 260
Further reading 261
Coding Theory (Code, Coding) 264
Further reading 264
Codon 265
Further reading 265
Codon Usage Bias 266
Further reading 267
Coevolution (Molecular Coevolution) 268
Further reading 268
Coevolution of Protein Residues 269
Further reading 269
Cofactor 271
COG, see Cluster of Orthologous Groups. 272
COGnitor, see Cluster of Orthologous Groups. 273
Coil (Random Coil) 274
Further reading 274
Coiled-Coil 275
Further reading 275
Coincidental Evolution, see Concerted Evolution. 277
Comparative Gene Prediction, see Gene Prediction, comparative. 278
Comparative Genomics 279
Further reading 280
Comparative Modeling (Homology Modeling, Knowledge-based Modeling) 281
Further reading 282
Complement 283
Complex Trait, see Multifactorial Trait. 284
Complexity 285
Further reading 285
Complexity Regularization, see Model Selection. 286
Components of Variance, see Variance Components. 287
Compound Similarity and Similarity Searching 288
Computational Biology, see Bioinformatics. 289
Computational Gene Annotation, see Gene Prediction. 290
Concept 291
Conceptual Graph 292
Concerted Evolution (Coincidental Evolution, Molecular Drive) 293
Further reading 293
Confidence, see Association Rule Mining. 295
Conformation 296
Further reading 296
Conformational Energy 297
Further reading 297
Conjugate Gradient Minimization, see Energy Minimization. 298
Connectionist Networks, see Neural Networks. 299
Consensus, see Consensus Sequence, Consensus Pattern, Consensus Tree. 300
Consensus Coding Sequence Database, see CCDS. 301
Consensus Pattern (Regular Expression, Regex) 302
Further reading 303
Consensus Pattern Rule 304
Further reading 305
Consensus Sequence 306
Further reading 307
Consensus Tree (Strict Consensus, Majority-Rule Consensus, Supertree) 309
Software 309
Further reading 310
Conservation (Percentage Conservation) 311
Further reading 311
Constraint-based Modeling (Flux Balance Analysis) 312
Further reading 313
Contact Map 315
Contig 316
Further reading 316
Continuous Trait, see Quantitative Trait. 317
Convergence 318
Further reading 318
Coordinate System of Sequences 319
Further reading 319
Copy Number Variation 321
Further reading 322
Core Consensus 323
Further reading 323
Correlation Analysis, see Regression Analysis, Association Rule Mining, Lift 324
COSMIC (Catalogue of Somatic Mutations in Cancer) 325
Further reading 326
Covariation Analysis 327
Further reading 329
CpG Island 331
Further reading 331
CRM, see Cis-regulatory Module. 332
Cross-Reference (Xref) 333
Cross-Validation (K-Fold Cross-Validation, Leave-One-Out, Jackknife, Bootstrap) 334
Further reading 334
C-Value, see Genome Size. 335
D 336
DAG, see Directed Acyclic Graph. 340
DAS Services 341
Data Definition Language, see Data Description Language. 342
Data Description Language (DDL, Data Definition Language) 343
Data Flow, see Stream Mining. 344
Data Integration 345
Further reading 345
Data Manipulation Language (DML) 346
Data Mining, see Pattern Analysis. 347
Data Pre-processing 348
Data Processing 349
Data Standards 350
Further reading 350
Data Standards in Proteomics 351
Further reading 352
Data Standards in Systems Modeling 353
Further reading 354
Data Structure (Array, Associative Array, Binary Tree, Hash, Linked List, Object, Record, Struct, Vector) 355
Data Stream, see Stream Mining. 357
Data Warehouse 358
Database (NoSQL, Quad Store, RDF Database, Relational Database, Triple Store) 360
Database of Genotypes and Phenotypes, see dbGAP. 362
Database Search Engine (Proteomics) (Peptide Spectrum Match, PSM) 363
Further reading 363
DataMonkey 364
Further reading 364
Dayhoff Amino Acid Substitution Matrix (PAM Matrix, Percent Accepted Mutation Matrix) 365
Further reading 366
dbEST 367
Further reading 367
dbGAP (the Database of Genotypes and Phenotypes) 368
Further reading 368
dbSNP 370
Further reading 371
dbSTS 372
Further reading 372
dbVar (Database of Genomic Structural Variation) 373
Further reading 374
DDBJ (DNA Databank of Japan) 375
Further reading 375
DDL, see Data Description Language. 377
De Novo Assembly in Next Generation Sequencing 378
Dead-End Elimination Algorithm 380
Further reading 381
Decision Surface 382
Further reading 382
Decision Tree 383
Decoy Database 384
Further reading 384
Degree of Genetic Determination, see Heritability. 385
Deletion, see Indel. 386
DELILA 387
Further reading 388
DELILA Instructions 389
Further reading 389
DendroPy 390
Further reading 390
Dependent Variable, see Label. 391
Description Logic (DL) 392
Descriptors, see Features. 393
DGV (Database of Genetic Variants) 394
Further reading 394
Diagnostic Performance, see Diagnostic Power. 396
Diagnostic Power (Diagnostic Performance, Discriminating Power) 397
Further reading 398
Dihedral Angle (Torsion Angle) 400
Dinucleotide Frequency 402
Further reading 402
DIP 403
Further reading 403
Directed Acyclic Graph (DAG) 404
Discrete Function Prediction (Function Prediction) 405
References 407
Discriminant Analysis, see Classification. 409
Discriminating Power, see Diagnostic Power. 410
Distance Matrix (Similarity Matrix) 411
Distances Between Trees (Phylogenetic Trees, Distance) 412
Software 412
Further reading 413
Distributed Computing 414
Disulphide Bridge 416
DL, see Description Logic. 417
DML, see Data Manipulation Language. 418
DNA Array, see Microarray. 419
DNA Databank of Japan, see DDBJ. 420
DNA-Protein Coevolution 421
Further reading 421
DNA Sequence 423
DNA Sequencing 424
DnaSP 425
Further reading 425
DOCK 426
Further reading 426
Docking 428
Further reading 428
Domain, see Protein Domain. 429
Domain Alignment, see Alignment. 430
Domain Family 431
Further reading 432
Dot Matrix, see Dot Plot. 434
Dot Plot (Dot Matrix) 435
Further reading 436
Dotter 437
Further reading 437
Downstream 438
Drug-Like 439
Further reading 439
DrugBank 441
Further reading 441
Druggability 442
Further reading 442
Druggable Genome (Druggable Proteome) 444
Further reading 444
DW, see Data Warehouse. 445
Dynamic Programming 446
Further reading 449
E 451
E-M Algorithm, see Expectation Maximization Algorithm. 454
E Value 455
Further reading 458
EBI (EMBL-EBI, European Bioinformatics Institute) 460
Further reading 461
EcoCyc 462
Further reading 462
EDA, see Estimation of Distribution Algorithm. 463
Edge (in a Phylogenetic Tree), see Branch (of a Phylogenetic Tree) (Edge, Arc). 464
EGASP, see GASP. 465
Electron Density Map 466
Further reading 467
Electrostatic Energy 468
Electrostatic Potential 469
ELIXIR (Infrastructure for Biological Information in Europe) 470
Elston-Stewart Algorithm (E-S Algorithm) 471
Further reading 472
EMA, EMAGE, see e-Mouse Atlas. 474
EMBL-Bank, see EMBL Nucleotide Sequence Database. 475
EMBL Database, see EMBL Nucleotide Sequence Database. 476
EMBL-EBI, see EBI. 477
EMBL Nucleotide Sequence Database (EMBL-Bank, EMBL Database) 478
Further reading 479
EMBnet (The Global Bioinformatics Network) (formerly the European Molecular Biology Network) 480
EMBOSS (The European Molecular Biology Open Software Suite) 482
Further reading 482
EMA, EMAGE e-Mouse Atlas of Gene Expression (EMAGE): e-Mouse Atlas (EMA) 483
Further reading 483
e-Mouse Atlas of Gene Expression (EMAGE), see e-Mouse Atlas. 484
emPAI (Exponentially Modified Protein Abundance Index) 485
Further reading 485
Empirical Pair Potentials 486
Further reading 486
Empirical Potential Energy Function 487
Further reading 488
ENA (European Nucleotide Archive) 489
Further reading 490
ENCODE (Encyclopedia of DNA Elements) 491
Further reading 492
ENCprime/SeqCount 493
Further reading 493
Encyclopedia of DNA Elements, see ENCODE. 494
End Gap 495
Energy Minimization 497
Further reading 499
Enhancer 500
Further reading 500
Ensembl 501
Ensembl Genome Browser, see Ensembl. 504
Ensembl Plants 505
Further reading 505
Ensembl Variation, see Ensembl. 506
Ensemble of Classifiers 507
Further reading 507
Entrez 508
Further reading 508
Entrez Gene (NCBI ‘Gene’) 509
Further reading 509
Entropy 511
Epaktolog (Epaktologue) 512
Further reading 513
Epistatic Interactions (Epistasis) 514
Further reading 515
Error 516
Further reading 516
Error Measures (Accuracy Measures, Performance Criteria, Predictive Power, Generalization) 517
Further reading 519
E-S Algorithm, see Elston-Stewart Algorithm. 520
EST, see Expressed Sequence Tag. 521
Estimation of Distribution Algorithm (EDA) 522
Further reading 522
Euclidean Distance 524
Eukaryote Organism and Genome Databases 525
EUPA (European Proteomics Association) 530
European Bioinformatics Institute, see EBI. 531
European Molecular Biology Open Software Suite, see EMBOSS. 532
European Nucleotide Archive, see ENA. 533
EuroPhenome 534
Further reading 534
Evolution 536
Further reading 536
Evolution of Biological Information 537
Further reading 537
Evolutionary Distance 538
Software 538
Further reading 538
Exclusion Mapping 539
Further reading 540
Exome Sequencing 541
Further reading 541
Exon 543
Further reading 543
Exon Shuffling 544
Further reading 544
Expectation Maximization Algorithm (E-M Algorithm) 545
Further reading 546
Exponentially Modified Protein Abundance Index, see emPAI. 547
Expressed Sequence Tag (EST) 548
Further reading 549
Expression Level (of Gene or Protein) 551
Extended Tracts of Homozygosity 552
Further reading 552
eXtensible Markup Language, see XML. 553
External Branch, see Branch of a Phylogenetic Tree. 554
External Node, see Node of a Phylogenetic Tree. 555
Extrinsic Gene Prediction, see Gene Prediction, homology-based. 556
F 557
F-Measure 559
Further reading 559
False Discovery Rate Control (False Discovery Rate, FDR) 561
Further reading 561
False Discovery Rate in Proteomics 563
Further reading 563
Family-based Association Analysis 564
Further reading 565
FASTA (FASTP) 567
Further reading 568
FASTP, see FASTA. 570
FDR, see False Discovery Rate Control. 571
Feature (Independent Variable, Predictor Variable, Descriptor, Attribute, Observation) 572
Further reading 572
Feature Subset Selection 573
Further reading 574
FGENES 576
Further reading 576
FigTree 578
Fingerprint (Chemoinformatics), see Chemical Hashed Fingerprint. 579
Fingerprint of Proteins 580
Further reading 581
Finite Mixture Model 583
Further reading 583
Fisher Discriminant Analysis (Linear Discriminant Analysis) 585
Further reading 586
Flat File Data Formats 587
FLUCTUATE, see LAMARC. 588
Flux Balance Analysis, see Constraint-based Modeling. 589
Flybase 590
Further reading 591
FLYBRAIN 592
Further reading 592
Fold 593
Further reading 594
Fold Library 595
Further reading 595
Foldback, see RNA hairpin. 596
Folding Free Energy 597
Further reading 597
Founder Effect 599
Further reading 599
Frame-based Language 600
Free R-Factor 601
Further reading 601
Frequent Itemset, see Association Rule Mining. 602
Frequent Sub-Graph, see Graph Mining. 603
Frequent Sub-Structure, see Graph Mining. 604
Function Prediction, see Discrete Function Prediction. 605
Functional Database 606
Further reading 606
Functional Genomics 607
Further reading 608
Functional Signature 610
Further reading 611
Functome 612
Further reading 612
Fuzzy Logic, see Fuzzy Set. 613
Fuzzy Set (Fuzzy Logic, Possibility Theory) 614
Further reading 615
G 616
GA, see Genetic Algorithm. 620
Gametic Phase Disequilibrium, see Linkage Disequilibrium. 621
Gap 622
Gap Penalty 623
Further reading 624
GARLI (Genetic Algorithm for Rapid Likelihood Inference) 625
Further reading 625
Garnier-Osguthorpe-Robson Method, see GOR Secondary Structure Prediction Method. 626
GASP (Genome Annotation Assessment Project, E-GASP) 627
Further reading 628
GBROWSE, see Gene Annotation, visualization tools 629
GC Composition, see Base Composition. 630
GC Richness, see Base Composition. 631
GEISHA 632
Further reading 632
GenBank 633
Further reading 634
GENCODE 635
Further reading 635
Gene Annotation 636
Further reading 636
Gene Annotation, formats 638
Gene Annotation, hand-curated 641
Further reading 641
Gene Annotation, visualization tools 643
Further reading 644
Gene Cluster 645
Further reading 645
Gene Dispensability 646
Further reading 646
Gene Distribution 648
Further reading 648
Gene Diversity 650
Further reading 650
Gene Duplication 652
Further reading 652
Gene Expression Database (GXD), see Mouse Genome Informatics. 654
Gene Expression Profile 655
Further reading 655
Gene Family 657
Further reading 658
Gene Finding, see Gene Prediction. 659
Gene-finding Format, see Gene Annotation, formats. 660
Gene Flow 661
Further reading 661
Gene Fusion Method 662
Further reading 662
Gene Index 663
Gene Neighbourhood 664
Further reading 664
Gene Ontology (GO) 665
Gene Ontology Consortium 666
Gene Prediction 667
Further reading 668
Gene Prediction, ab initio 670
Further reading 673
Gene Prediction, accuracy 677
Further reading 678
Gene Prediction, alternative splicing 680
Further reading 680
Gene Prediction, comparative 682
Further reading 684
Gene Prediction, homology-based (Extrinsic Gene Prediction, Look-Up Gene Prediction) 686
Further reading 687
Gene Prediction, NGS-based 690
Further reading 690
Gene Prediction, non-canonical 692
Further reading 693
Gene Prediction, pipelines 695
Further reading 696
Gene Size 698
Further reading 698
Gene Symbol 700
Gene Symbol, human 701
Gene Transfer Format, see Gene Annotation, formats 702
Genealogical Sorting Index (gsi) 703
Further reading 704
GeneChip, see Affymetrix GeneChip™ Oligonucleotide Microarray. 705
GENEID 706
Further reading 707
General Feature Format, see Gene Annotation, Formats. 709
Generalization, see Error Measures. 710
Genetic Algorithm (GA) 711
Further reading 712
Genetic Code (Universal Genetic Code, Standard Genetic Code) 713
Further reading 714
Genetic Linkage, see Linkage 715
Genetic Network 716
Further reading 717
Genetic Redundancy 718
Further reading 718
Genetic Variation, see Variation (Genetic). 719
GENEWISE 720
Further reading 721
Genome Annotation 722
Further reading 723
Genome Annotation Assessment Project, see GASP. 725
Genome Scans for Linkage (Genome-Wide Scans) 726
Further reading 726
Genome Size (C-Value) 728
Further reading 728
Genome-Wide Association Study (GWAS) 729
Further reading 730
Genome-Wide Scans (linkage), see Genome Scans 731
Genome-Wide Survey 732
Further reading 733
GENOMEGRAPHS, see Gene Annotation, visualization tools. 734
Genomics 735
Further reading 736
Genotype Imputation 737
Further reading 738
GENSCAN 739
Further reading 740
GFF, see Gene Annotation, formats. 742
GFF2PS, see Gene Annotation, visualization tools. 743
GFF3, see Gene Annotation, formats. 744
Gibbs Sampling, see Markov Chain Monte Carlo. 745
Global Alignment 746
Further reading 746
Global Organisation for Bioinformatics Learning, Education & Training (GOBLET), see BTN.
Globular 748
GO, see Gene Ontology. 749
GOBASE (Organelle Genome Database) 750
Further reading 750
GOBLET, see BTN. 751
GOBO, see Global Open Biology Ontologies. 752
GOR Secondary Structure Prediction Method (Garnier-Osguthorpe-Robson Method) 753
Further reading 753
Gradient Descent (Steepest Descent Method) 754
Further reading 754
GRAIL 755
Further reading 756
GRAIL Description Logic 757
Gramene 758
Further reading 758
Graph Mining (Frequent Sub-Graph, Frequent Sub-Structure) 759
Graph Representation of Genetic, Molecular and Metabolic Networks 760
Further reading 762
Group I Intron, see Intron. 763
Group II Intron, see Intron. 764
GTF, see Gene Annotation, formats. 765
Guilt by Association Annotation, see Annotation Transfer. 766
Gumball Machine 767
Further reading 767
GWAS, see Genome-Wide Association Study. 768
GWAS Central 769
Further reading 769
H 771
h2, see Heritability. 774
Hand-curated Gene Annotation, see Gene Annotation, hand-curated. 775
Haplotype 776
Further reading 777
HapMap Project 779
Further reading 779
Hardy-Weinberg Equilibrium 781
Further reading 781
Haseman-Elston Regression (HE-SD, HE-SS, HE-CP and HE-COM) 782
Further reading 783
Hash, see Data Structure. 785
HAVANA (Human and Vertebrate Analysis and Annotation) 786
HE-COM, HE-CP, HE-SD, HE-SS, see Haseman-Elston Regression 787
Helical Wheel 788
Further reading 789
Heritability (h2, Degree of Genetic Determination) 790
Further reading 791
Heterotachy 792
Software 792
Further reading 792
HGMD (Human Gene Mutation Database) 794
Further reading 795
HGT, see Horizontal Gene Transfer. 796
HGVBASE, see GWAS Central. 797
Hidden Markov Model (HMM, Hidden Semi-Markov Models, Profile Hidden Markov Models, Training of Hidden Markov Models, Dynamic Programming, Pair Hidden Markov Models) 798
Further reading 801
Hierarchy 803
High-Scoring Segment Pair (HSP) 804
Further reading 804
HIV RT and Protease Sequence Database, see STanford HIV RT and Protease Sequence Database. 806
HIV Sequence Database 807
Further reading 807
HMM, see Hidden Markov Model. 808
HMMer 809
Further reading 809
Homologous Genes 810
Homologous Superfamily 811
Further reading 811
Homology 813
Further reading 814
Homology Modeling, see Comparative Modeling. 816
Homology Search 817
Further reading 819
Homology-based Gene Prediction, see Gene Prediction, homology-based. 821
Homozygosity Mapping 822
Further reading 823
Horizontal Gene Transfer (HGT) 824
Further reading 824
HSP, see High-scoring Segment Pair. 826
HTU, see Hypothetical Taxonomic Unit. 827
HUGO (The Human Genome Organization) 828
Human-Curated Gene Annotation, see Gene Annotation, hand-curated. 830
Human Gene Mutation Database, see HGMD. 831
Human Genome Variation Database, see HGVBASE. 832
Human Proteome Organization, see HUPO. 833
Human Variome Project (HVP) 834
Further reading 834
HUPO (Human Proteome Organization) 835
HVP, see Human Variome Project. 836
Hydrogen Bond 837
Hydropathy 838
Further reading 839
Hydropathy Profile (Hydrophobicity Plot, Hydrophobic Plot) 841
Further reading 843
Hydrophilicity 844
Hydrophobic Moment 845
Hydrophobic Scale 846
Hydrophobicity Plot, see Hydropathy Profile. 847
HyPhy (Hypothesis Testing Using Phylogenies) 848
Hypothetical Taxonomic Unit (HTU) 849
I 850
IBD, see Identical by Descent. 853
IBS, see Identical by State. 854
IC50, see Binding Affinity. 855
ICA, see Independent Component Analysis. 856
Identical by Descent (Identity by Descent, IBD) 857
Further reading 857
Identical by State (Identity by State, IBS) 859
Further reading 859
IGV, see Gene Annotation, visualization tools. 860
IMa2 (Isolation with Migration a2) 861
Further reading 861
IMGT (International Immunogenetics Database) 862
Further reading 862
Imprinting 863
Further reading 864
Imputation, see Genotype Imputation. 865
InChI (International Chemical Identifier) 866
InChi Key 867
Indel (Insertion-Deletion Region, Insertion, Deletion, Gap) 868
Further reading 869
Independent Component Analysis (ICA) 870
Further reading 870
Independent Variables, see Features. 872
Individual (Instance) 873
Individual Information 874
Further reading 874
Information 875
Information Retrieval, see Text Mining. 876
Information Theory 877
Further reading 877
Initiator Sequence 878
Further reading 878
INPPO (International Plant Proteomics Organization) 879
Insertion, Insertion-Deletion Region, see Indel. 881
Instance, see Individual. 882
Instance-based Learner, see K-Nearest Neighbor Classification. 883
Integrated Gene Annotation Pipelines, see Gene Prediction, Pipelines. 884
Integrated Gene Prediction Systems, see Gene Prediction Systems, Pipelines. 885
Intelligent Data Analysis, see Pattern Analysis. 886
Interactome 887
Further reading 888
Intergenic Sequence 889
Further reading 889
Interior Branch, Internal Branch, see Branch and Phylogenetic Tree. 890
Interior Node, Internal Node, see Node and Phylogenetic Tree. 891
International Chemical Identifier, see InChi. 892
International Immunogenetics Database, see IMGT. 893
International Plant Proteomics Organization, see INPPO. 894
International Society for Computational Biology (ISCB) 895
Interolog (Interologue) 897
Further reading 897
InterPro 898
Further reading 899
InterProScan, see InterPro. 901
Interspersed Sequence (Long-Term Interspersion, Long-Period Interspersion, Short-Term Interspersion, Short-Period Interspersion, Locus Repeat) 902
Further reading 902
Intrinsic Gene Prediction, see Gene Prediction, ab initio. 903
Intron 904
Further reading 904
Intron Phase 905
Further reading 905
IR, see Text Mining. 906
ISCB, see International Society for Computational Biology. 907
Isobaric Tagging 908
Isochore 909
Further reading 909
IsomiR 910
Further reading 910
Iteration 911
IUPAC-IUB Codes (Nucleotide Base Codes, Amino Acid Abbreviations) 912
Further reading 914
J 915
Jaccard Distance (Jaccard Index, Jaccard Similarity Coefficient) 916
Jackknife 917
JASPAR 918
Further reading 918
JELLYFISH 919
Further reading 919
jModelTest 920
Further reading 920
Jpred, see Web-based Secondary Structure Prediction Programs. 921
Jumping Gene, see Transposable Element. 922
Junk DNA 923
Further reading 924
K 926
K-Fold Cross-Validation, see Cross-Validation. 928
K-Means Clustering, see Clustering. 929
K-Medoids 930
Further reading 930
K-Nearest Neighbor Classification (Lazy Learner, KNN, Instance-based Learner) 932
Further reading 932
Kappa Virtual Dihedral Angle 933
Karyotype 934
Further reading 934
Kd, see Binding Affinity. 935
Kernel-based Learning Method, see Kernel Method. 936
Kernel Function 937
Further reading 938
Kernel Machine, see Kernel Method. 939
Kernel Method (Kernel Machine, Kernel-based Learning Method) 940
Further reading 941
Ki, see Binding Affinity. 943
KIF, see Knowledge Interchange Format. 944
Kin Selection 945
Further reading 945
Kinetic Modeling 946
Further reading 947
Kinetochore 948
Further reading 948
Kingdom 949
Further reading 950
KNN, see K-Nearest Neighbor Classification, Lazy Learner, Instance-based Learner. 951
Knowledge 952
Knowledge Base 953
Knowledge-based Modeling, see Homology Modeling. 954
Knowledge Interchange Format (KIF) 955
Further reading 955
Knowledge Map, see Bayesian Network. 956
Knowledge Representation Language (KRL) 957
Further reading 959
Kozak Sequence 960
Further reading 960
KRL, see Knowledge Representation Language. 961
L 962
L-G Algorithm, see Lander-Green Algorithm. 964
Label (Labeled Data, Response, Dependent Variable) 965
Further reading 965
Labeled Data, see Label. 966
Labeled Tree 967
Laboratory Information Management System (LIMS) 968
Further reading 968
LAMARC 970
Further reading 970
Lander-Green Algorithm (L-G Algorithm) 971
Further reading 972
Lattice 974
Lazy Learner, see K-Nearest Neighbor Classification. 975
LD, see Linkage Disequilibrium. 976
Lead Optimization 977
Leaf, see Node and Phylogenetic Tree. 978
Leave-One-Out Validation, see Cross-Validation. 979
Leiden Open Variation Database, see Locus-Specific Database. 980
Lexicon 981
Ligand Efficiency 982
Further reading 982
LIMS, see Laboratory Information Management System. 983
LINE (Long Interspersed Nuclear Element) 984
Further reading 984
Linear Discriminant Analysis, see Fisher Discriminant Analysis. 986
Linear Regression and Non-Linear Regression, see Regression Analysis. 987
Linkage (Genetic Linkage) 988
Further reading 989
Linkage Analysis 990
Further reading 991
Linkage Disequilibrium (LD, Gametic Phase Disequilibrium, Allelic Association) 993
Further reading 994
Linkage Disequilibrium Analysis, see Association Analysis. 996
Linkage Disequilibrium Map 997
Further reading 997
Linked Data 999
Further reading 999
Linked List, see Data Structure. 1000
Lipinski Rule of Five, see Rule of Five. 1001
Local Alignment (Local Similarity) 1002
Further reading 1002
Local Similarity, see Local Alignment. 1004
Locus Repeat, see Interspersed Sequence. 1005
Locus-Specific Database (Locus-Specific Mutation Database, LSDB) 1006
Further reading 1006
LOD Score (Logarithm of Odds Score) 1007
Further reading 1008
Log Odds Score, see Amino Acid Exchange Matrix, LOD Score. 1010
LogDet, see Paralinear Distance. 1011
Logical Modeling of Genetic Networks 1012
Further reading 1014
Logo, see Sequence Logo. 1015
LogP (ALogP, CLogP) 1016
Long-Period Interspersion, see Interspersed Sequence. 1017
Long-Term Interspersion, see Interspersed Sequence. 1018
Look-Up Gene Prediction, see Gene Prediction, Homology-based. 1019
Loop 1020
Further reading 1020
Loop Prediction/Modeling 1021
Further reading 1021
LOVD, see Locus-Specific Database. 1023
Low Complexity Region 1024
Further reading 1025
LSDB, see Locus-Specific Database. 1026
M 1027
MacClade 1032
Further reading 1032
Machine Learning 1033
Further reading 1034
Majority-Rule Consensus Tree, see Consensus Tree. 1035
Mammalian Gene Collection, see MGC. 1036
Mammalian Promoter Database, see MpromDB. 1037
Manual Gene Annotation, see Gene Annotation (hand-curated). 1038
Map Function 1039
Further reading 1040
Mapping by Admixture Linkage Disequilibrium, see Admixture Mapping. 1041
Mark-up Language 1042
Further reading 1042
Marker 1044
Further reading 1045
Markov Chain 1046
Markov Chain Monte Carlo (MCMC, Metropolis-Hastings, Gibbs Sampling) 1047
Markov Model, see Hidden Markov Model, Markov Chain. 1048
Mathematical Modeling (of Molecular/Metabolic/Genetic Networks) 1049
Further reading 1054
Mature microRNA 1055
Maximal Margin Classifier, see Support Vector Machine. 1056
Maximum Likelihood Phylogeny Reconstruction 1057
Software 1057
Further reading 1058
Maximum Parsimony Principle (Parsimony, Occam's Razor) 1059
Software 1060
Further reading 1060
MaxQuant 1062
Further reading 1062
MCMC, see Markov Chain Monte Carlo. 1063
MEGA (Molecular Evolutionary Genetics Analysis) 1064
Further reading 1064
Mendelian Disease 1065
Further reading 1066
MEROPS 1067
Further reading 1067
Mesquite 1068
Message 1069
Further reading 1069
Metabolic Modeling 1070
Metabolic Network 1071
Further reading 1071
Metabolic Pathway 1073
Further reading 1073
Metabolome (Metabonome) 1074
Further reading 1074
Metabolomics Databases 1076
Further reading 1077
Metabolomics Software 1079
Further reading 1082
Metabonome, see Metabolome. 1083
Metadata 1084
Metropolis-Hastings, see Markov Chain Monte Carlo. 1085
MGC (Mammalian Gene Collection) 1086
Further reading 1086
MGD (Mouse Genome Database) 1087
Further reading 1087
MGED Ontology 1089
Microarray 1090
Further reading 1091
Microarray Image Analysis 1092
Further reading 1092
Microarray Normalization 1094
Further reading 1095
Microfunctionalization 1097
Further reading 1097
MicroRNA 1098
MicroRNA Discovery 1099
Further reading 1100
MicroRNA Family 1102
Further reading 1102
MicroRNA Prediction, see MicroRNA Discovery. 1104
MicroRNA Seed 1105
MicroRNA Seed Family, see MicroRNA Family. 1106
MicroRNA Target 1107
Further reading 1107
MicroRNA Target Prediction 1109
Further reading 1110
Microsatellite 1111
Further reading 1112
Midnight Zone 1113
Further reading 1113
MIGRATE-N 1115
Further reading 1115
MIME Types 1116
Further reading 1118
Minimum Evolution Principle 1119
Software 1119
Further reading 1119
Minimum Information Models 1121
Further reading 1121
Minisatellite 1123
Further reading 1123
miRBase 1124
Further reading 1124
Mirtron 1126
Further reading 1126
Missing Data, see Missing Value. 1128
Missing Value (Missing Data) 1129
Further reading 1129
Mitelman Database (Chromosome Aberrations and Gene Fusions in Cancer) 1131
Further reading 1131
Mixture Models 1132
Software 1132
Further reading 1132
MM, see Markov Chain. 1134
MOD, see Model Organism Database. 1135
Model Order Selection, see Model Selection. 1136
Model Organism Database (MOD) 1137
Further reading 1137
Model Selection (Model Order Selection, Complexity Regularization) 1139
Further reading 1139
Modeling, Macromolecular 1140
Further reading 1141
Models, Molecular 1142
Further reading 1145
Modeltest 1147
Further reading 1147
ModENCODE, see ENCODE. 1148
Modular Protein 1149
Module Shuffling 1150
Further reading 1150
Mol Chemical Representation Format 1151
Molecular Clock (Evolutionary Clock, Rate of Evolution) 1152
Software 1152
Further reading 1153
Molecular Coevolution, see Coevolution. 1154
Molecular Drive, see Concerted Evolution. 1155
Molecular Dynamics Simulation 1156
Further reading 1156
Molecular Efficiency 1157
Further reading 1158
Molecular Evolutionary Mechanisms 1160
Further reading 1162
Molecular Information Theory 1163
Further reading 1163
Molecular Machine 1164
Further reading 1164
Molecular Machine Capacity 1165
Further reading 1165
Molecular Machine Operation 1166
Further reading 1166
Molecular Mechanics 1167
Further reading 1167
MOLECULAR NETWORK, see Network. 1168
Molecular Replacement 1169
Further reading 1170
Monophyletic Group, see Clade. 1171
Monte Carlo Simulation 1172
Further reading 1172
Motif 1173
Further reading 1174
Motif Discovery 1175
Further reading 1176
Motif Enrichment Analysis 1177
Further reading 1178
Motif Search 1179
Further reading 1183
Mouse Genome Database, see Mouse Genome Informatics. 1187
Mouse Genome Informatics (MGI, Mouse Genome Database, MGD) 1188
Further reading 1188
Mouse Tumor Biology (MTB) Database, see Mouse Genome Informatics. 1189
MouseCyc, see Mouse Genome Informatics. 1190
MPromDB (Mammalian Promoter Database) 1191
Further reading 1191
MrBayes 1192
Further reading 1193
Multidomain Protein 1194
Multifactorial Trait (Complex Trait) 1195
Further reading 1195
Multifurcation (Polytomy) 1197
Multilabel Classification 1198
Further reading 1198
Multilayer Perceptron, see Neural Network. 1200
Multiple Alignment 1201
Further reading 1205
MULTIPLE HIERARCHY (Polyhierarchy) 1208
Multiplex Sequencing 1209
Multipoint Linkage Analysis 1210
Further reading 1211
Murcko Framework, see Bemis and Murcko Framework. 1212
Mutation Matrix, see Amino Acid Exchange Matrix. 1213
N 1214
N-terminus (amino terminus) 1216
Naïve Bayes, see Bayesian Classifier. 1217
National Center for Biotechnology Information, see NCBI. 1218
Natural Selection 1219
Further reading 1219
NCBI (National Center for Biotechnology Information) 1221
Further reading 1222
NDB, see Nucleic Acid Database. 1223
Nearest Neighbor Methods 1224
Further reading 1224
Nearly Neutral Theory, see Neutral Theory. 1225
Needleman-Wunsch Algorithm 1226
Further reading 1226
Negative Selection, see Purifying Selection. 1227
Negentropy (Negative Entropy) 1228
Further reading 1228
Neighbor-Joining Method 1229
Software 1229
Further reading 1229
Network (Genetic Network, Molecular Network, Metabolic Network) 1230
Further reading 1234
Neural Network (Artificial Neural Network, Connectionist Network, Backpropagation Network, Multilayer Perceptron) 1235
Further reading 1237
Neutral Theory (Nearly Neutral Theory) 1239
Further reading 1239
Newton-Raphson Minimization, see Energy Minimization. 1241
Next Generation DNA Sequencing 1242
Next Generation Sequencing, De Novo Assembly, see De Novo Assembly in Next Generation Sequencing. 1245
Nit 1246
Further reading 1246
NMR (Nuclear Magnetic Resonance) 1247
Node, see Phylogenetic Tree. 1249
Noise (Noisy Data) 1250
Further reading 1250
Non-Crystallographic Symmetry, see Space Group. 1251
Non-Parametric Linkage Analysis, see Allele-Sharing Methods. 1252
Non-Synonymous Mutation 1253
NOR, see Nucleolar Organizer Region. 1254
NoSQL, see Database. 1255
Nuclear Intron, see Intron. 1256
Nuclear Magnetic Resonance, see NMR. 1257
Nucleic Acid Database (NDB) 1258
Further reading 1258
Nucleic Acid Sequence Databases 1260
Further reading 1260
Nucleolar Organizer Region (NOR) 1261
Further reading 1261
Nucleotide Base Codes, see IUPAC-IUB Codes. 1262
O 1263
OBF (The Open Bioinformatics Foundation) 1265
Object, see Data Structure. 1266
Object-Relational Database 1267
OBO-Edit 1268
Further reading 1268
OBO Foundry 1269
Further reading 1269
Observation, see Feature. 1270
Occam's Razor, see Parsimony. 1271
ODB (Operon DataBase) 1272
Further reading 1272
Offspring Branch (Daughter Branch/Lineage) 1273
OKBS, see Open Knowledge Base Connectivity. 1274
Oligo Selection Program, see OSP. 1275
Oligogenic Effect, see Oligogenic Inheritance. 1276
Oligogenic Inheritance (Oligogenic Effect) 1277
Further reading 1277
Omics 1278
Further reading 1278
OMIM (Online Mendelian Inheritance in Man) 1279
Further reading 1279
Online Mendelian Inheritance in Man, see OMIM. 1280
Ontology 1281
Further reading 1281
Open Biological and Biomedical Ontologies, see OBO Foundry. 1283
Open Reading Frame (ORF) 1284
Open Reading Frame Finder, see ORF Finder. 1285
Open Regulatory Annotation Database, see OregAnno. 1286
Operon DataBase, see OPD. 1287
Open Source Bioinformatics Organizations 1288
Operating System 1289
Operational Taxonomic Unit (OTU) 1291
OPLS 1292
Further reading 1292
Optimal Alignment 1293
Further reading 1293
Oral Bioavailability 1294
ORF, see Open Reading Frame. 1295
ORegAnno (Open Regulatory Annotation Database) 1296
Further reading 1296
ORFan, see Orphan Gene. 1298
Organelle Genome Database, see GOBASE. 1299
Organism-Specific Database, see MOD. 1300
Organismal Classification, see Taxonomic Classification. 1301
Orphan Gene (ORFan) 1302
Further reading 1302
Ortholog (Orthologue) 1303
Further reading 1303
Outlier, see Outlier Mining. 1305
Outlier Mining (Outlier) 1306
Further reading 1307
Overdominance 1308
Further reading 1308
Overfitting (Overtraining) 1309
Further reading 1309
Overtraining, see Overfitting. 1310
OWL, see Web Ontology Language. 1311
P 1312
Pairwise Alignment 1317
Further reading 1318
PAM Matrix (of Amino Acid Substitutions), see Dayhoff Amino Acid Substitution Matrix, Amino Acid Exchange Matrix. 1319
PAM Matrix of Nucleotide Substitutions (Point Accepted Mutations) 1320
Further reading 1320
PAML (Phylogenetic Analysis by Maximum Likelihood) 1321
Further reading 1321
Paralinear Distance (LogDet) 1323
Further reading 1323
Parallel Computing in Phylogenetics 1324
Further reading 1324
Paralog (Paralogue) 1326
Parameter 1328
Parametric Bootstrapping, see Bootstrapping. 1329
Paraphyletic Group, see Cladistics. 1330
Parent, see Template. 1331
Parity Bit 1332
Parsimony 1334
Further reading 1335
Partition Coefficient, see LogP. 1336
Pattern 1337
Pattern Analysis 1338
Further reading 1338
Pattern Discovery, see Motif Discovery. 1339
Pattern of Change Analysis, see Phylogenetic Events Analysis. 1340
Pattern Recognition, see Pattern Analysis. 1341
PAUP* (Phylogenetic Analysis Using Parsimony (and Other Methods)) 1342
Further reading 1342
PAZAR 1343
Further reading 1343
Pearson Correlation, see Regression Analysis. 1344
Penalty, see Gap Penalty. 1345
Penetrance 1346
Further reading 1346
Peptide 1347
Further reading 1347
Peptide Bond (Amide Bond) 1348
Further reading 1348
Peptide Mass Fingerprint 1349
Peptide Spectrum Match (PSM) 1350
PeptideAtlas 1351
Further reading 1351
Percent Accepted Mutation Matrix, see Dayhoff Amino Acid Substitution Matrix. 1352
Petri Net 1353
Further reading 1353
Pfam 1355
Further reading 1356
PFM, see Position-Frequency Matrix. 1357
Phantom Indel (Frame Shift) 1358
Pharmacophore 1359
Phase (Sensu Linkage) 1360
Further reading 1361
PheGenI, see dbGAP. 1363
PHRAP 1364
PHRED 1365
Further reading 1365
PHYLIP (PHYLogeny Inference Package) 1366
Further reading 1366
Phylogenetic Events Analysis (Pattern of Change Analysis) 1368
Further reading 1371
Phylogenetic Footprint 1372
Phylogenetic Footprint Detection 1373
Further reading 1374
Phylogenetic Placement of Short Reads 1375
Software 1375
Further reading 1376
Phylogenetic Profile 1377
Further reading 1377
Phylogenetic Reconstruction, see Phylogenetic Tree. 1378
Phylogenetic Shadowing, see Phylogenetic Footprinting. 1379
Phylogenetic Tree (Phylogeny, Phylogeny Reconstruction, Phylogenetic Reconstruction) 1380
Further reading 1386
Phylogenetic Trees, Distance, see Distances Between Trees. 1390
Phylogenetics 1391
Phylogenomics 1392
Further reading 1392
Phylogeny, Phylogeny Reconstruction, see Phylogenetic Tree. 1394
Piecewise-Linear Models 1395
Further reading 1395
PIPMAKER 1397
Further reading 1397
PlantsDB 1398
Further reading 1398
Plesiomorphy 1399
Further reading 1399
Point Accepted Mutations, see PAM Matrix of Nucleotide Substitutions. 1400
Polar 1401
Polarization 1402
Further reading 1402
Polygenic Effect, see Polygenic Inheritance. 1403
Polygenic Inheritance (Polygenic Effect) 1404
Further reading 1404
Polymorphism (Genetic Polymorphism) 1405
Further reading 1406
Polypeptide 1407
Further reading 1407
Polyphyletic Group, see Cladistics. 1408
Polytomy, see Multifurcation. 1409
PomBase 1410
Further reading 1410
Population Bottleneck (Bottleneck) 1411
Further reading 1411
Position-Specific Scoring Matrix, see Profile. 1413
Position Weight Matrix 1414
Position Weight Matrix of Transcription Factor Binding Sites 1415
Further reading 1416
Positional Candidate Approach 1418
Further reading 1418
Positive Classification 1420
Further reading 1420
Positive Darwinian Selection (Positive Selection) 1422
Further reading 1423
Positive Selection, see Positive Darwinian Selection. 1424
Post-Order Tree Traversal, see Tree Traversal. 1425
Posterior Error Probability (PEP) 1426
Further reading 1426
Potential of Mean Force 1427
Power Law (Zipf's Law) 1428
Further reading 1428
Prediction of Gene Function 1429
Further reading 1431
Predictive ADME (Absorption, Distribution, Metabolism, and Excretion), see Chemoinformatics. 1432
PRIDE 1433
Further reading 1433
PRIMER3 1434
Further reading 1434
Principal Components Analysis (PCA) 1435
Further reading 1435
PRINTS 1436
Further reading 1437
Probabilistic Network, see Bayesian Network. 1439
ProDom 1440
Further reading 1440
Profile (Weight Matrix, Position Weight Matrix, Position-Specific Scoring Matrix, PSSM) 1442
Further reading 1443
Profile, 3D 1444
Profile Searching 1446
Further reading 1449
Programming and Scripting Languages 1451
Promoter 1453
Further reading 1453
The Promoter Database of Saccharomyces cerevisiae (SCPD) 1454
Further reading 1454
Promoter Prediction 1455
Further reading 1456
PROSITE 1458
Further reading 1459
Protégé 1460
Protein Array (Protein Microarray) 1461
Further reading 1461
Protein Data Bank (PDB) 1463
Further reading 1464
Protein Databases 1465
Further reading 1465
Protein Domain 1466
Protein Family 1467
Further reading 1468
Protein Family and Domain Signature Databases 1469
Further reading 1469
Protein Fingerprint, see Fingerprint. 1471
Protein Inference Problem 1472
Further reading 1472
Protein Information Resource (PIR) 1473
Further reading 1473
Protein Microarray, see Protein Array. 1474
Protein Module 1475
Further reading 1475
Protein-Protein Coevolution 1476
Further reading 1476
Protein-Protein Interaction Network Inference 1478
Further reading 1478
Protein Sequence, see Sequence of Protein. 1480
Protein Sequence Cluster Databases 1481
Further reading 1481
Protein Structure 1482
Further reading 1483
Protein Structure Classification Databases, see Structure 3D Classification. 1484
Proteome 1485
Further reading 1486
Proteome Analysis Database (Integr8) 1488
Further reading 1488
Proteomics 1489
Further reading 1490
Proteomics Standards Initiative (PSI) 1491
Proteotypic Peptide 1492
Further reading 1492
Pseudoparalog (pseudoparalogue) 1493
Further reading 1493
Pseudogene 1494
Further reading 1495
PSI BLAST 1496
Further reading 1496
PSSM, see Profile. 1498
Purifying Selection (Negative Selection) 1499
Further reading 1499
Q 1500
Qindex (Qhelix Qstrand
Further reading 1501
QM/MM Simulations 1502
Further reading 1502
QSAR (Quantitative Structure Activity Relationship) 1503
Further reading 1503
Qualitative and Quantitative Databases used in Systems Biology 1504
Further reading 1505
Qualitative Differential Equations 1506
Further reading 1506
Quantitative Proteomics 1507
Quantitative Trait (Continuous Trait) 1509
Further reading 1510
Quartets, Phylogenetic 1512
Software 1512
Further reading 1512
Quartet Puzzling, see Quartet, Phylogenetic. 1514
Quaternary Structure 1515
R 1516
R-Factor 1519
Further reading 1519
r8s 1520
Further reading 1520
Ramachandran Plot 1521
Further reading 1522
Random Forest 1523
Further reading 1523
Random Trees 1525
Further reading 1525
Rat Genome Database (RGD) 1526
Further reading 1526
Rate Heterogeneity 1527
Software 1527
Further reading 1527
Rational Drug Design, see Structure-based Drug Design. 1529
RDF 1530
RDF Database, see Database. 1531
readseq 1532
Reasoning 1533
Recombination 1534
Further reading 1535
RECOMBINE, see LAMARC. 1536
Record, see Data Structure. 1537
Recursion 1538
Reference Genome (Type Genome) 1539
Reference Sequence Database, see RefSeq. 1540
Refinement 1541
Further reading 1542
RefSeq (the Reference Sequence Database) 1543
Further reading 1543
Regex, see Regular Expresssion. 1544
Regression Analysis 1545
Further reading 1545
Regression Tree 1546
Further reading 1546
Regular Expression (Regex) 1548
Further reading 1549
Regularization (Ridge, Lasso, Elastic Net, Fused Lasso, Group Lasso) 1550
Further reading 1551
Regulatory Motifs in Network Biology 1553
Further reading 1554
Regulatory Network Inference 1555
Further reading 1556
Regulatory Region 1557
Regulatory Region Prediction 1558
Further reading 1559
Regulatory Sequence, see Transcriptional Regulatory Region. 1561
Regulome 1562
Relational Database 1563
Relational Database Management System (RDBMS) 1564
Relationship 1565
REPEATMASKER 1566
Repeats Alignment, see Alignment. 1567
Repetitive Sequences, see Simple DNA Sequence. 1568
Residue, see Amino Acid. 1569
Resolution in X-Ray Crystallography 1570
Further reading 1571
Response, see Label. 1572
RESTful Web Services 1573
Restriction Map 1574
Retrosequence 1575
Further reading 1575
Retrotransposon 1576
Further reading 1577
Reverse Complement 1578
Rfam 1579
Further reading 1579
Rfrequency 1580
Further reading 1580
RGD, see Rat Genome Database. 1581
Ri 1582
Further reading 1582
RIBOSOMAL RNA (rRNA) 1583
Further reading 1589
Ribosome Binding Site (RBS) 1591
Further reading 1591
RMSD, see Root Mean Square Deviation. 1592
RNA (General Categories) 1593
Further reading 1597
RNA Folding 1599
RNA Hairpin 1600
Further reading 1600
RNA-seq 1601
RNA Splicing, see Splicing. 1603
RNA Structure 1604
Further reading 1608
RNA Structure Prediction (Comparative Sequence Analysis) 1609
Further reading 1610
RNA Structure Prediction (Energy Minimization) 1611
Further reading 1612
RNA Tertiary Structure Motifs 1614
Further reading 1617
Robustness 1621
Further reading 1622
ROC Curve 1623
Further reading 1624
Role 1625
Root Mean Square Deviation (RMSD) 1626
Further reading 1626
Rooted Phylogenetic Tree, see Phylogenetic Tree. Contrast with Unrooted Phylogenetic Tree. 1628
Rooting Phylogenetic Trees 1629
Further reading 1629
Rosetta Stone Method 1631
Further reading 1632
Rotamer 1633
Further reading 1633
Rough Set 1634
rRNA, see Ribosomal RNA. 1635
Rsequence 1636
Further reading 1636
Rule 1637
Further reading 1637
Rule Induction 1639
Further reading 1639
Rule of Five (Lipinski Rule of Five) 1641
Further reading 1641
S 1642
Saccharomyces Genome Database, see SGD. 1648
Safe Zone 1649
Further reading 1649
SAGE (Serial Analysis of Gene Expression) 1650
Further reading 1650
SAR (Structure–Activity Relationship) 1652
Scaffold 1653
Further reading 1653
Scaled Phylogenetic Tree, see Branch. Contrast with Unscaled Phylogenetic Tree. 1654
Schematic (Ribbon, Cartoon) Models 1655
Further reading 1655
Scientific Workflows 1657
Further reading 1657
Score 1658
Further reading 1658
Scoring Matrix (Substitution Matrix) 1659
Further reading 1660
SCWRL 1662
Further reading 1662
SDF 1663
Search by Signal, see Sequence Motifs: prediction and modeling. 1664
Second Law of Thermodynamics 1665
Further reading 1666
Secondary Structure of Protein 1667
Further reading 1667
Secondary Structure Prediction of Protein 1668
Further reading 1669
Secretome 1670
Further reading 1670
Segmental Duplication 1672
Further reading 1672
Segregation Analysis 1674
Further reading 1675
Selected Reaction Monitoring (SRM) 1677
Further reading 1677
Selenoprotein 1678
Further reading 1678
Self-Consistent Mean Field Algorithm 1680
Further reading 1680
Self-Organizing Map (SOM, Kohonen Map) 1682
Further reading 1682
Semantic Network 1683
Semi-Global Alignment, see Global Alignment. 1684
Seq-Gen 1685
Further reading 1685
SeqCount, see ENCprime. 1686
Sequence Alignment 1687
Sequence Assembly 1688
Sequence Complexity (Sequence Simplicity) 1689
Further reading 1689
Sequence Conservation, see Conservation. 1690
Sequence Distance Measures 1691
Software 1691
Further reading 1692
Sequence Logo 1693
Further reading 1694
Sequence Motif, see Motif. 1695
Sequence Motifs: Prediction and Modeling (Search by Signal) 1696
Further reading 1700
Sequence of a Protein 1702
Sequence Pattern 1703
Further reading 1703
Sequence Read Archive (SRA, Short Read Archive) 1704
Further reading 1704
Sequence Retrieval System, see SRS. 1705
Sequence Similarity 1706
Further reading 1707
Sequence Similarity-based Gene Prediction, see Gene Prediction, homology-based. 1708
Sequence Similarity Search 1709
Sequence Simplicity, see Sequence Complexity. 1711
Sequence Tagged Site (STS) 1712
Sequence Walker 1713
Further reading 1715
Serial Analysis of Gene Expression, see SAGE. 1717
SGD (Saccharomyces Genome Database) 1718
Further reading 1718
Shannon Entropy (Shannon Uncertainty) 1719
Further reading 1719
Shannon Sphere 1720
Further reading 1721
Shannon Uncertainty, see Shannon Entropy. 1722
Short-Period Interspersion, Short-Term Interspersion, see Interspersed Sequence. 1723
Short Read Archive, see Sequence Read Archive. 1724
Shuffle Test 1725
Side Chain 1726
Further reading 1726
Side-Chain Prediction 1727
Further reading 1727
Signal-to-Noise Ratio, see Noise. 1729
Signature, see Fingerprint. 1730
SILAC, see Stable Isotope Labelling with Amino Acids in Cell Culture. 1731
Silent Mutation, see Synonymous Mutation. 1732
Similarity Index, see Distance Matrix. 1733
SIMPLE (SIMPLE34) 1734
Further reading 1734
Simple DNA Sequence (Simple Repeat, Simple Sequence Repeat) 1735
Further reading 1735
Simple Repeat, see Simple DNA Sequence. 1736
Simple Sequence Repeat, see Simple DNA Sequence. 1737
SIMPLE34, see SIMPLE. 1738
Simulated Annealing 1739
Further reading 1739
Simultaneous Alignment and Tree Building 1740
Software 1740
Further reading 1740
Single Nucleotide Polymorphism (SNP) 1741
Further reading 1742
Sippl Test, see Ungapped Threading Test B. 1743
Sister Group 1744
Site, see Character. 1745
SITES 1746
Further reading 1746
Small Sample Correction 1747
Further reading 1747
SMILES 1748
Further reading 1748
Smith-Waterman 1749
Further reading 1749
SNP, see Single Nucleotide Polymorphism. 1750
Software Suites for Regulatory Sequences 1751
Solanaceae Genomics Network (SGN) 1752
Further reading 1752
Solvation Free Energy 1753
Further reading 1753
SOV 1754
Further reading 1755
Space-Filling Model 1756
Further reading 1757
SPARQL (SPARQL Protocol and RDF Query Language) 1758
Spliced Alignment 1759
Further reading 1760
Splicing (RNA Splicing) 1761
Further reading 1761
Split (Bipartition) 1762
Spotted cDNA Microarray 1763
Further reading 1764
SQL (Structured Query Language) 1765
SRA, see Sequence Read Archive. 1766
SRS (Sequence Retrieval System) 1767
Further reading 1767
Stable Isotope Labelling with Amino Acids in Cell Culture (SILAC) 1768
STADEN 1769
Further reading 1769
Standard Genetic Code, see Genetic Code. 1770
Standardized Qualitative Dynamical Systems 1771
Further reading 1772
Stanford HIV RT and Protease Sequence Database (HIV RT and Protease Sequence Database) 1773
Further reading 1773
Start Codon, see Genetic Code. 1775
Statistical Mechanics 1776
Statistical Potential Energy 1777
Further reading 1777
Steepest Descent Method, see Gradient Descent. 1779
Stem-loop, see RNA hairpin. 1780
Stochastic Process 1781
Stop Codon, see Genetic Code. 1782
Stream Mining (Time Series, Sequence, Data Stream, Data Flow) 1783
Further reading 1784
Strict Consensus Tree, see Consensus Tree. 1785
Structural Alignment 1786
Further reading 1787
Structural Genomics 1788
Further reading 1789
Structural Motif 1791
Structurama 1792
Further reading 1792
Structure 1793
Further reading 1793
Structure–3D Classification 1794
Further reading 1795
Structure-Activity Relationship, see SAR. 1796
Structure-based Drug Design (Rational Drug Design) 1797
Further reading 1797
STS, see Sequence Tagged Site. 1798
Subfunctionalization 1799
Further reading 1799
Substitution Process 1801
Further reading 1801
Subtree 1802
Superfamily 1803
Further reading 1803
Superfold 1805
Further reading 1805
Supermatrix Approach 1807
Software 1807
Further reading 1807
Supersecondary Structure 1809
Further reading 1809
Supertree, see Consensus Tree. 1810
Supervised and Unsupervised Learning 1811
Further reading 1811
Support Vector Machine (SVM, Maximal Margin Classifier) 1812
Further reading 1813
Surface Models 1814
Further reading 1815
Surprisal 1816
Further reading 1816
SVM, see Support Vector Machine. 1817
Swiss-Prot, see UniProt. 1818
SwissModel 1819
Further reading 1819
Symmetry Paradox 1820
Further reading 1821
Synapomorphy 1822
Further reading 1822
Synonymous Mutation (Silent Mutation) 1823
Synteny 1824
Further reading 1825
Systems Biology 1826
Further reading 1826
T 1827
Tandem Mass Spectrometry (MS) 1830
Tandem Repeat 1831
Further reading 1831
Tanimoto Distance 1832
Target 1833
TATA BOX 1834
Further reading 1834
Taxonomic Classification (Organismal Classification) 1835
Further reading 1836
Taxonomic Unit 1838
Taxonomy 1839
Telomere 1840
Further reading 1840
Template (Parent) 1841
Template Gene Prediction, see Gene Prediction, ab initio. 1842
Term 1843
Terminology 1844
Text Mining (Information Retrieval, IR) 1845
Further reading 1846
Thermal Noise 1847
Further reading 1847
Thesaurus 1848
Thousand Genomes Project 1849
Further reading 1849
THREADER, see Threading. 1850
Threading 1851
Further reading 1851
TIM-barrel 1852
Trace Archive 1853
Further reading 1853
Tracer 1854
Trans-Proteomic Pipeline (TPP) 1855
Further reading 1855
Transaction Database (Data Warehouse) 1856
Transcription 1857
Further reading 1857
Transcription Factor 1858
Further reading 1858
Transcription Factor Binding Motif (TFBM) 1859
Further reading 1859
Transcription Factor Binding Site 1860
Transcription Factor Database 1862
Transcription Start Site (TSS) 1864
Further reading 1864
Transcriptional Regulatory Region (Regulatory Sequence) 1865
Further reading 1865
Transcriptome 1866
Further reading 1867
TRANSFAC 1868
Further reading 1868
TRANSFER RNA (tRNA) 1870
Further reading 1872
Translation 1873
Further reading 1873
Translation End Site 1874
Further reading 1874
Translation Start Site 1876
Further reading 1876
Translatome 1878
Further reading 1878
Transposable Element (Transposon) 1880
Further reading 1881
Transposon, see Transposable Element. 1882
Tree, see Phylogenetic Tree. 1883
Tree of Life 1884
Further reading 1884
Tree-based Progressive Alignment 1885
Further reading 1885
Tree-Puzzle, see Quartets, Phylogenetic. 1887
TreeStat 1888
Tree Topology 1889
Tree Traversal 1891
TreeView X 1892
Further reading 1892
Trinucleotide Repeat 1893
Further reading 1893
Triple Store, see Database. 1894
tRNA, see Transfer RNA. 1895
Turn 1896
Further reading 1896
Twilight Zone 1897
Further reading 1898
Two-Dimensional Gel Electrophoresis (2DE) 1899
Further reading 1900
Type Genome see Reference Genome 1901
U 1902
UCSC Genome Browser 1903
Further reading 1904
Uncertainty 1905
Ungapped Threading Test B (Sippl Test) 1906
Unigene 1907
Further reading 1907
UniProt 1908
Universal Genetic Code, see Genetic Code. 1909
Unsupervised Learning, see Supervised and Unsupervised Learning. 1910
Unrooted Phylogenetic Tree, see Phylogenetic Tree. 1911
Unscaled Phylogenetic Tree, see Branch. 1912
UPGMA 1913
Further reading 1913
Upstream 1914
V 1915
Validation Measures for Clustering 1916
Further reading 1916
Variance Components (Components of Variance, VC) 1918
Further reading 1920
Variation (Genetic) 1921
VarioML 1922
Further reading 1922
Vector Alignment Search Tool: VAST (Vector Alignment Search Tool) 1923
Further reading 1923
VC, see Variance Components. 1925
Vector, see Data Structure. 1926
Vector Alignment Search Tool, see VAST. 1927
VecScreen 1928
VectorNTI 1929
Vertebrate Genome Annotation Database: VEGA (Vertebrate Genome Annotation Database) 1930
Further reading 1930
Vertebrate Genome Annotation Database, see VEGA. 1931
Virtual Library 1932
Virtual Screening 1933
Virtualization 1934
VISTA 1936
Further reading 1936
Visualization, Molecular 1937
Further reading 1939
Visualization of Multiple Sequence Alignments – Physicochemical Properties 1940
Further reading 1942
W 1943
Web Ontology Language (OWL) 1944
Web Services 1945
Weight Matrix, see Sequence Motifs: Prediction and Modeling. 1946
Whatcheck 1947
Further reading 1947
WhatIf 1948
Further reading 1948
WormBase 1949
Further reading 1949
WSDL/SOAP Web Services 1950
X 1951
X-Ray Crystallography for Structure Determination 1952
Further reading 1952
X Chromosome, see Sex Chromosome. 1954
Xenbase 1955
Further reading 1955
Xenolog (Xenologue) 1956
XML (eXtensible Markup Language) 1957
Further reading 1959
Y 1960
Yeast Deletion Project (YDPM) 1961
Further reading 1961
Yule Process 1962
Z 1963
z-score 1964
Zero Base, see Zero Coordinate. 1965
Zero Base Zero Position: Zero Coordinate (Zero Base, Zero Position) 1966
Zero Position, see Zero Coordinate. 1967
Zeta Virtual Dihedral Angle 1968
Zipf's Law, see Power Law. 1969
Author Index 1970
End User License Agreement 2024

Rezensionen

"This book is an invaluable resource for students,
researchers, and academics. Summing Up: Highly
recommended. Upper-division undergraduates through
professionals/practitioners." (Choice, 1
September 2014)

Produkt-Details

• Erscheint lt. Verlag: 2.6.2014
• Sprache: englisch
• Themenwelt: Schulbuch / Wörterbuch ► Lexikon / Chroniken
• Themenwelt: Mathematik / Informatik ► Informatik ► Theorie / Studium
• Themenwelt: Mathematik / Informatik ► Mathematik ► Angewandte Mathematik
• Themenwelt: Naturwissenschaften ► Biologie ► Genetik / Molekularbiologie
• Themenwelt: Technik
• Schlagworte: author • Bioinformatics • Bioinformatics & Computational Biology • Bioinformatik • Bioinformatik u. Computersimulationen in der Biowissenschaften • Biology • biomedical engineering • Biomedizintechnik • Biowissenschaften • Colour • Computational • Computational Bioengineering • Computational Biology • computationbased • concentrating • concerned • contributors • entries • facing p • Field • Fields • Index • Ix • Life Sciences • List • Mathematics • Mathematik • Mathematik in der Biologie • molecular • Plate • Rechnergestütztes Bioengineering • Rechnergestütztes Bioengineering • Research • section • similar • specifically • within
• ISBN-10: 1-118-59815-6 / 1118598156
• ISBN-13: 978-1-118-59815-3 / 9781118598153