Concise Encyclopaedia of Bioinformatics and Computational Biology (eBook)

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

eBook Download: PDF

2013 | 2. Auflage
John Wiley & Sons (Verlag)
978-1-118-59816-0 (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.

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

Concise Encyclopaedia of Bioinformatics and Computational Biology 1
Title Page 5
Copyright 6
Contents 
9 
List of Contributors 11
Preface 15
A 17
Ab Initio 19
Ab Initio Gene Prediction, see Gene Prediction, ab initio. 19
ABNR, see Energy Minimization. 19
Accuracy (of Protein Structure Prediction) 19
David Jones 19
Accuracy Measures, see Error Measures. 20
Adjacent Group 20
Aidan Budd and Alexandros Stamatakis 20
Admixture Mapping (Mapping by Admixture Linkage Disequilibrium) 21
Andrew Collins, Mark McCarthy and Steven Wiltshire 21
Adopted-basis Newton– 
22 
Affine Gap Penalty, see Gap Penalty. 22
Affinity Propagation-based Clustering 22
Pedro Larran 
22 
Affymetrix GeneChip™ Oligonucleotide Microarray 23
Stuart Brown and Dov Greenbaum 23
Affymetrix Probe Level Analysis 24
Stuart Brown 24
After Sphere, see After State. 25
After State (After Sphere) 25
Thomas D. Schneider 25
AIC, see Akaike Information Criterion. 25
Akaike Information Criterion 26
Pedro Larranaga and Concha Bielza 26
Algorithm 26
Matthew He 26
Alignment (Domain Alignment, Repeats Alignment) 27
Jaap Heringa 27
Alignment Score 29
Laszlo Patthy 29
Allele-Sharing Methods (Non-parametric Linkage Analysis) 30
Mark McCarthy, Steven Wiltshire and Andrew Collins 30
Allelic Association 31
Mark McCarthy, Steven Wiltshire and Andrew Collins 31
Allen Brain Atlas 32
Dan Bolser 32
Allopatric Evolution (Allopatric Speciation) 33
A.R. Hoelzel 33
Allopatric Speciation, see Allopatric Evolution. 33
AlogP 33
Bissan Al-Lazikani 33
Alpha carbon, see Ca (C-Alpha). 34
Alpha Helix 34
Roman Laskowski and Tjaart de Beer 34
Alternative Splicing 34
Enrique Blanco and Josep F. Abril 34
Alternative Splicing Gene Prediction, see Gene Prediction, alternative splicing. 35
Amide Bond (Peptide Bond) 35
Roman Laskowski and Tjaart de Beer 35
Amino Acid (Residue) 36
Roman Laskowski, Jeremy Baum and Tjaart de Beer 36
Amino Acid Abbreviations, see IUPAC-IUB Codes. 37
Amino Acid Composition 37
Jeremy Baum 37
Amino Acid Exchange Matrix (Dayhoff Matrix, Log Odds Score, PAM (Matrix), BLOSUM Matrix) 37
Jaap Heringa 37
AMINO Acid Substitution Matrix, see Amino Acid Exchange Matrix. 38
Amino-terminus, see N-terminus. 39
Amphipathic 39
Roman Laskowski and Tjaart de Beer 39
Analog (Analogue) 39
Dov Greenbaum 39
Ancestral Lineage, see Offspring Lineage. 40
Ancestral State Reconstruction 40
Sudhir Kumar and Alan Filipski 40
Anchor Points 41
Roland Dunbrack 41
Annotation Refinement Pipelines, see Gene Prediction. 41
Annotation Transfer (Guilt by Association Annotation) 41
Dov Greenbaum 41
APBIONET (Asia-Pacific Bioinformatics Network) 42
Pedro Fernandes 42
Apomorphy 42
A.R. Hoelzel 42
APOLLO, see Gene Annotation, visualization tools. 43
Arc, see Branch (of a Phylogenetic Tree). 43
Are We There Yet?, see AWTY. 43
Aromatic 43
Roman Laskowski and Tjaart de Beer 43
Array, see Data Structure. 44
Artificial Neural Networks, see Neural Networks. 44
ASBCB (The African Society for Bioinformatics and Computational Biology) 44
Pedro Fernandes 44
Association Analysis (Linkage Disequilibrium Analysis) 45
Andrew Collins, Mark McCarthy and Steven Wiltshire 45
Association Rule, see Association Rule Mining. 46
Association Rule Mining (Frequent Itemset, Association Rule, Support, Confidence, Correlation Analysis) 46
Feng Chen and Yi-Ping Phoebe Chen 46
Associative Array, see Data Structure. 48
Asymmetric Unit 48
Liz Carpenter 48
Atomic Coordinate File (PDB file) 48
Eric Martz 48
Autapomorphy 49
A.R. Hoelzel 49
Autozygosity, see Homozygosity, Homozygosity Mapping. 49
AWTY (Are We There Yet?) 49
Michael P. Cummings 49
Axiom 50
Robert Stevens 50
B 51
Backbone (Main Chain) 53
Roman Laskowski and Tjaart de Beer 53
Backbone Models 53
Eric Martz 53
Backpropagation Networks, see Neural Networks. 54
Bagging 54
Concha Bielza and Pedro Larranaga 54
Ball and Stick Models 55
Eric Martz 55
BAMBE (Bayesian Analysis in Molecular Biology and Evolution) 56
Michael P. Cummings 56
Base-Call Confidence Values 56
Rodger Staden and John M. Hancock 56
Base Composition (GC Richness, GC Composition) 57
Katheleen Gardiner 57
Bayes' 
57 
Feng Chen, Yi-Ping Phoebe Chen and Matthew He 57
Bayesian Classifier (Naive Bayes) 58
Pedro Larranaga and Concha Bielza 58
Bayesian Evolutionary Analysis Utility, see BEAUti. 59
Bayesian Information Criterion (BIC) 59
Concha Bielza and Pedro Larranaga 59
Bayesian Network (Belief Network, Probabilistic Network, Causal Network, Knowledge Map) 60
John M Hancock 60
Bayesian Phylogenetic Analysis 60
Sudhir Kumar and Alan Filipski 60
BEAGLE 61
Michael P. Cummings 61
Beam Search 62
Concha Bielza and Pedro Larranaga 62
BEAST (Bayesian Evolutionary Analysis by Sampling Trees) 62
Michael P. Cummings 62
BEAUti (Bayesian Evolutionary Analysis Utility) 63
Michael P. Cummings 63
Before State (Before Sphere) 63
Thomas D. Schneider 63
Belief Network, see Bayesian Network. 64
Bemis and Murcko Framework (Murcko Framework) 64
Bissan Al-Lazikani 64
Best-First Search 65
Concha Bielza and Pedro Larranaga 65
Beta Barrel 65
Roman Laskowski 65
Beta Breaker 65
Patrick Aloy 65
Beta Sheet 66
Roman Laskowski and Tjaart de Beer 66
Beta Strand 66
Roman Laskowski and Tjaart de Beer 66
BIC, see Bayesian Information Criterion. 66
Biclustering Methods 67
Pedro Larran 
67 
Bifurcation (in a Phylogenetic Tree) 67
Aidan Budd and Alexandros Stamatakis 67
Binary Numerals 68
John M. Hancock 68
Binary Relation 68
Robert Stevens 68
Binary Tree, see Data Structure. 68
Binding Affinity (Kd, Ki, IC50) 68
Bissan Al-Lazikani and John M. Hancock 68
Binding Site 69
Thomas D. Schneider 69
Binding Site Symmetry 69
Thomas D. Schneider 69
Bio++ 72
Michael P. Cummings 72
Bioactivity Database 72
Bissan Al-Lazikani 72
Bioinformatics (Computational Biology) 73
John M. Hancock 73
The Bioinformatics Organization, Inc (formerly bioinformatics.org) 74
Pedro Fernandes 74
Bioinformatics Training Network, see BTN. 74
Biological Identifiers 74
Carole Goble and Katy Wolstencroft 74
BioMart 75
Obi L. Griffith and Malachi Griffith 75
Bipartition, see Split 76
Bit 76
Thomas D. Schneider 76
BLAST (Maximal Segment Pair, MSP) 77
Jaap Heringa 77
BLASTX 79
Roderic Guigo 79
BLAT (BLAST-like Alignment Tool) 80
J.M. Hancock 80
BLOSUM (BLOSUM Matrix) 80
Laszlo Patthy 80
Boltzmann Factor 81
Roman Laskowski and Tjaart de Beer 81
Boolean Logic 81
James Marsh, David Thorne and Steve Pettifer 81
Boosting 82
Concha Bielza and Pedro LarranËœ aga 82
Bootstrap Analysis, see Bootstrapping. 82
Bootstrapping (Bootstrap Analysis) 82
Aidan Budd and Alexandros Stamatakis 82
Bottleneck, see Population Bottleneck. 84
Box 84
Thomas D. Schneider 84
Branch (of a Phylogenetic Tree) (Edge, Arc) 85
Aidan Budd and Alexandros Stamatakis 85
Branch Length, see Branch, Branch-length Estimation. 85
Branch-length Estimation 85
Sudhir Kumar and Alan Filipski 85
BTN (Bioinformatics Training Network) 86
Pedro Fernandes 86
C 87
C-a 
91 
Cancer Gene Census (CGC) 91
Malachi Griffith and Obi L. Griffith 91
Candidate Gene (Candidate Gene-based Analysis) 91
Mark McCarthy, Steven Wiltshire and Andrew Collins 91
Carboxy-Terminus, see C-Terminus. 92
CASP 92
David Jones 92
Catalogue of Somatic Mutations in Cancer, see COSMIC 93
Catalytic Triad 93
Roman Laskowski and Tjaart de Beer 93
Category 94
Robert Stevens 94
Causal Network, see Bayesian Network 95
CCDS (Consensus Coding Sequence Database) 95
Obi L. Griffith and Malachi Griffith 95
CDS, see Coding Region. 95
Centimorgan 95
Katheleen Gardiner 95
Centromere (Primary Constriction) 95
Katheleen Gardiner 95
CGC, see Cancer Gene Census. 96
Channel Capacity (Channel Capacity Theorem) 96
Thomas D. Schneider 96
Character (Site) 97
Sudhir Kumar and Alan Filipski 97
CHARMM 97
Roland Dunbrack 97
Chemical Biology 98
Bissan Al-Lazikani 98
Chemical Hashed Fingerprint 98
Bissan Al-Lazikani 98
Chemoinformatics 99
Bissan Al-Lazikani 99
ChIP-seq 99
Stuart Brown 99
Chou & Fasman Prediction Method
Patrick Aloy 100
Chromatin 101
Katheleen Gardiner 101
Chromosomal Deletion 101
Katheleen Gardiner 101
Chromosomal Inversion 101
Katheleen Gardiner 101
Chromosomal Translocation 102
Katheleen Gardiner 102
Chromosome 102
Katheleen Gardiner 102
Chromosome Band 103
Katheleen Gardiner 103
Circos, see Gene Annotation, visualization tools. 103
Cis-regulatory Element 103
Jacques van Helden 103
Cis-regulatory Module (CRM) 104
Jacques van Helden 104
Cis-regulatory Module Prediction 104
Jacques van Helden 104
Clade (Monophyletic Group) 105
Aidan Budd and Alexandros Stamatakis 105
Cladistics 105
Aidan Budd and Alexandros Stamatakis 105
Clan 106
Aidan Budd and Alexandros Stamatakis 106
Classification 106
Robert Stevens 106
Classification in Machine Learning (Discriminant Analysis) 107
Nello Cristianini 107
Classifier (Reasoner) 107
Robert Stevens 107
Classifiers, Comparison 107
Pedro Larran 
107 
Clogp 
108 
Bissan Al-Lazikani 108
CLUSTAL 109
Jaap Heringa 109
Clustal Omega, see Clustal. 110
ClustalW, see Clustal 110
ClustalX, see Clustal. 110
Cluster 110
Dov Greenbaum 110
Cluster Analysis, see Clustering. 111
Cluster of Orthologous Groups (COG, COGnitor) 111
Dov Greenbaum 111
Clustering (Cluster Analysis) 112
Nello Cristianini 112
Clustering Analysis, see Clustering. 113
CNS 113
Roland Dunbrack 113
Code, Coding, see Coding Theory. 113
Coding Region (CDS) 114
Roderic Guigo 114
Coding Region Prediction 114
Roderic Guigo 114
Coding Statistics (Coding Measure, Coding Potential, Search by Content) 115
Roderic Guigo 115
Coding Theory (Code, Coding) 117
Thomas D. Schneider 117
Codon 117
Niall Dillon 117
Codon Usage Bias 118
Roderic Guigo 118
Coevolution (Molecular Coevolution) 119
Laszlo Patthy 119
Coevolution of Protein Residues 119
Laszlo Patthy 119
Cofactor 120
COG, see Cluster of Orthologous Groups. 120
COGnitor, see Cluster of Orthologous Groups. 120
Coil (Random Coil) 120
Roman Laskowski and Tjaart de Beer 120
Coiled-Coil 121
Patrick Aloy 121
Coincidental Evolution, see Concerted Evolution. 121
Comparative Gene Prediction, see Gene Prediction, comparative. 121
Comparative Genomics 121
Jean-Michel Claverie 121
Comparative Modeling (Homology Modeling, Knowledge-based Modeling) 123
Roland Dunbrack 123
Complement 124
John M. Hancock 124
Complex Trait, see Multifactorial Trait. 124
Complexity 124
Thomas D. Schneider 124
Complexity Regularization, see Model Selection. 124
Components of Variance, see Variance Components. 124
Compound Similarity and Similarity Searching 125
Bissan Al-Lazikani 125
Computational Biology, see Bioinformatics. 125
Computational Gene Annotation, see Gene Prediction. 125
Concept 125
Robert Stevens 125
Conceptual Graph 126
Robert Stevens 126
Concerted Evolution (Coincidental Evolution, Molecular Drive) 126
Dov Greenbaum 126
Confidence, see Association Rule Mining. 127
Conformation 127
Roman Laskowski and Tjaart de Beer 127
Conformational Energy 127
Roland Dunbrack 127
Conjugate Gradient Minimization, see Energy Minimization. 128
Connectionist Networks, see Neural Networks. 128
Consensus, see Consensus Sequence, Consensus Pattern, Consensus Tree. 128
Consensus Coding Sequence Database, see CCDS. 128
Consensus Pattern (Regular Expression, Regex) 128
Teresa K. Attwood 128
Consensus Pattern Rule 129
Teresa K. Attwood 129
Consensus Sequence 130
Dov Greenbaum and Thomas D. Schneider 130
Consensus Tree (Strict Consensus, Majority-Rule Consensus, Supertree) 132
Sudhir Kumar and Alan Filipski 132
Conservation (Percentage Conservation) 133
Dov Greenbaum 133
Constraint-based Modeling (Flux Balance Analysis) 133
Neil Swainston 133
Contact Map 134
Andrew Harrison and Christine Orengo 134
Contig 135
Rodger Staden 135
Continuous Trait, see Quantitative Trait. 135
Convergence 135
Dov Greenbaum 135
Coordinate System of Sequences 136
Thomas D. Schneider 136
Copy Number Variation 136
Dov Greenbaum 136
Core Consensus 137
Thomas D. Schneider 137
Correlation Analysis, see Regression Analysis, Association Rule Mining, Lift 138
COSMIC (Catalogue of Somatic Mutations in Cancer) 138
Malachi Griffith and Obi L. Griffith 138
Covariation Analysis 139
Jamie J. Cannone and Robin R. Gutell 139
CpG Island 141
Katheleen Gardiner 141
CRM, see Cis-regulatory Module. 141
Cross-Reference (Xref) 142
Cross-Validation (K-Fold Cross-Validation, Leave-One-Out, Jackknife, Bootstrap) 142
C-Value, see Genome Size. 142
D 143
DAG, see Directed Acyclic Graph. 145
DAS Services 145
Carole Goble and Katy Wolstencroft 145
Data Definition Language, see Data Description Language. 145
Data Description Language (DDL, Data Definition Language) 145
Matthew He 145
Data Flow, see Stream Mining. 145
Data Integration 146
Carole Goble and Katy Wolstencroft 146
Data Manipulation Language (DML) 146
Matthew He 146
Data Mining, see Pattern Analysis. 146
Data Pre-processing 146
Feng Chen and Yi-Ping Phoebe Chen 146
Data Processing 147
Matthew He 147
Data Standards 147
John M. Hancock 147
Data Standards in Proteomics 147
Juan Antonio Vizcaino 
147 
Data Standards in Systems Modeling 148
Juan Antonio Vizcaino 
148 
Data Stream, see Stream Mining. 149
Data Structure (Array, Associative Array, Binary Tree, Hash, Linked List, Object, Record, Struct, Vector) 149
David Thorne, Steve Pettifer and James Marsh 149
Data Warehouse 150
Carole Goble, Katy Wolstencroft and Matthew He 150
Database (NoSQL, Quad Store, RDF Database, Relational Database, Triple Store) 151
David Thorne, Steve Pettifer and James Marsh 151
Database of Genotypes and Phenotypes, see dbGAP. 152
Database Search Engine (Proteomics) (Peptide Spectrum Match, PSM) 152
Simon Hubbard 152
DataMonkey 153
Michael P. Cummings 153
Dayhoff Amino Acid Substitution Matrix (PAM Matrix, Percent Accepted Mutation Matrix) 153
Laszlo Patthy 153
dbEST 154
Guenter Stoesser 154
dbGAP (the Database of Genotypes and Phenotypes) 155
Malachi Griffith and Obi L. Griffith 155
dbSNP 155
Guenter Stoesser, Obi L. Griffith and Malachi Griffith 155
dbSTS 156
Guenter Stoesser 156
dbVar (Database of Genomic Structural Variation) 157
Malachi Griffith and Obi L. Griffith 157
DDBJ (DNA Databank of Japan) 157
Guenter Stoesser, Obi L. Griffith and Malachi Griffith 157
DDL, see Data Description Language. 158
De Novo Assembly in Next Generation Sequencing 158
Stuart Brown 158
Dead-End Elimination Algorithm 159
Roland Dunbrack 159
Decision Surface 160
Concha Bielza and Pedro Larranaga 
160 
Decision Tree 160
Feng Chen and Yi-Ping Phoebe Chen 160
Decoy Database 161
Simon Hubbard 161
Degree of Genetic Determination, see Heritability. 162
Deletion, see Indel. 162
DELILA 162
Thomas D. Schneider 162
DELILA Instructions 162
Thomas D. Schneider 162
DendroPy 163
Michael P. Cummings 163
Dependent Variable, see Label. 163
Description Logic (DL) 163
Robert Stevens 163
Descriptors, see Features. 164
DGV (Database of Genetic Variants) 164
Malachi Griffith and Obi L. Griffith 164
Diagnostic Performance, see Diagnostic Power. 165
Diagnostic Power (Diagnostic Performance, Discriminating Power) 165
Teresa K. Attwood 165
Dihedral Angle (Torsion Angle) 166
Roman Laskowski and Tjaart de Beer 166
Dinucleotide Frequency 167
Katheleen Gardiner 167
DIP 167
Patrick Aloy 167
Directed Acyclic Graph (DAG) 168
Robert Stevens 168
Discrete Function Prediction (Function Prediction) 168
Juan Antonio Garcia Ranea 168
Discriminant Analysis, see Classification. 170
Discriminating Power, see Diagnostic Power. 170
Distance Matrix (Similarity Matrix) 170
John M. Hancock 170
Distances Between Trees (Phylogenetic Trees, Distance) 171
Aidan Budd and Alexandros Stamatakis 171
Distributed Computing 172
Steve Pettifer, James Marsh and David Thorne 172
Disulphide Bridge 173
Jeremy Baum 173
DL, see Description Logic. 173
DML, see Data Manipulation Language. 173
DNA Array, see Microarray. 173
DNA Databank of Japan, see DDBJ. 173
DNA-Protein Coevolution 173
Laszlo Patthy 173
DNA Sequence 174
John M. Hancock and Rodger Staden 174
DNA Sequencing 174
Rodger Staden 174
DnaSP 174
Michael P. Cummings 174
DOCK 175
Marketa J. Zvelebil 175
Docking 176
Marketa J. Zvelebil 176
Domain, see Protein Domain. 176
Domain Alignment, see Alignment. 176
Domain Family 176
Teresa K. Attwood 176
Dot Matrix, see Dot Plot. 178
Dot Plot (Dot Matrix) 178
Jaap Heringa 178
Dotter 179
John M. Hancock and M.J. Bishop 179
Downstream 179
Niall Dillon 179
Drug-Like 179
Bissan Al-Lazikani 179
DrugBank 180
Dan Bolser 180
Druggability 180
Bissan Al-Lazikani 180
Druggable Genome (Druggable Proteome) 181
Bissan Al-Lazikani 181
DW, see Data Warehouse. 181
Dynamic Programming 181
Jaap Heringa 181
E 185
E-M Algorithm, see Expectation Maximization Algorithm. 187
E Value 187
Jaap Heringa 187
EBI (EMBL-EBI, European Bioinformatics Institute) 190
Guenter Stoesser, Obi L. Griffith and Malachi Griffith 190
EcoCyc 191
Robert Stevens 191
EDA, see Estimation of Distribution Algorithm. 191
Edge (in a Phylogenetic Tree), see Branch (of a Phylogenetic Tree) (Edge, Arc). 192
EGASP, see GASP. 192
Electron Density Map 192
Liz Carpenter 192
Electrostatic Energy 193
Roland Dunbrack 193
Electrostatic Potential 193
Jeremy Baum 193
ELIXIR (Infrastructure for Biological Information in Europe) 193
Pedro Fernandes 193
Mark McCarthy, Steven Wiltshire and Andrew Collins 194
EMA, EMAGE, see e-Mouse Atlas. 195
EMBL Database, see EMBL Nucleotide Sequence Database. 195
EMBL-EBI, see EBI. 195
EMBL Nucleotide Sequence Database (EMBL-Bank, EMBL Database) 196
Guenter Stoesser 196
EMBnet (The Global Bioinformatics Network) (formerly the European Molecular Biology Network) 197
Pedro Fernandes 197
EMBOSS (The European Molecular Biology Open Software Suite) 197
John M. Hancock and M.J. Bishop 197
e-Mouse Atlas (EMA) 198
Dan Bolser 198
e-Mouse Atlas of Gene Expression (EMAGE), see e-Mouse Atlas. 198
emPAI (Exponentially Modified Protein Abundance Index) 199
Simon Hubbard 199
Empirical Pair Potentials 199
Patrick Aloy 199
Empirical Potential Energy Function 200
Roland Dunbrack 200
ENA (European Nucleotide Archive) 201
Obi L. Griffith and Malachi Griffith 201
ENCODE (Encyclopedia of DNA Elements) 201
Enrique Blanco and Josep F. Abril 201
ENCprime/SeqCount 201
Michael P. Cummings 202
Encyclopedia of DNA Elements, see ENCODE. 203
End Gap 203
Jaap Heringa 203
Energy Minimization 204
Roland Dunbrack 204
Enhancer 205
Niall Dillon 205
Ensembl 206
Guenter Stoesser, Obi L. Griffith and Malachi Griffith 206
Ensembl Genome Browser, see Ensembl. 207
Ensembl Plants 207
Dan Bolser 207
Ensembl Variation, see Ensembl. 208
Ensemble of Classifiers 208
Concha Bielza and Pedro Larranaga 
208 
Entrez 208
Dov Greenbaum and John M. Hancock 208
Entrez Gene (NCBI 'Gene' 
209 
Malachi Griffith and Obi L. Griffith 209
Entropy 209
Thomas D. Schneider 209
Epaktolog (Epaktologue) 210
Laszlo Patthy 210
Epistatic Interactions (Epistasis) 210
Dov Greenbaum 210
Error 211
Thomas D. Schneider 211
Error Measures (Accuracy Measures, Performance Criteria, Predictive Power, Generalization) 212
Nello Cristianini 212
E-S Algorithm, see Elston-Stewart Algorithm. 213
EST, see Expressed Sequence Tag. 213
Estimation of Distribution Algorithm (EDA) 213
Pedro Larranaga 
213 
Euclidean Distance 214
John M. Hancock 214
Eukaryote Organism and Genome Databases 215
Dan Bolser 215
EUPA (European Proteomics Association) 217
Pedro Fernandes 217
European Bioinformatics Institute, see EBI. 217
European Molecular Biology Open Software Suite, see EMBOSS. 217
European Nucleotide Archive, see ENA. 217
EuroPhenome 217
John M. Hancock 217
Evolution 218
A.R. Hoelzel 218
Evolution of Biological Information 219
Thomas D. Schneider 219
Evolutionary Distance 219
Sudhir Kumar and Alan Filipski 219
Exclusion Mapping 220
Mark McCarthy, Steven Wiltshire and Andrew Collins 220
Exome Sequencing 221
Andrew Collins 221
Exon 221
Niall Dillon and Laszlo Patthy 221
Exon Shuffling 222
Austin L. Hughes and Laszlo Patthy 222
Expectation Maximization Algorithm (E-M Algorithm) 222
Mark McCarthy, Steven Wiltshire and Andrew Collins 222
Exponentially Modified Protein Abundance Index, see emPAI. 223
Expressed Sequence Tag (EST) 223
Jean-Michel Claverie 223
Expression Level (of Gene or Protein) 225
Matthew He 225
Extended Tracts of Homozygosity 225
Andrew Collins 225
eXtensible Markup Language, see XML. 226
External Branch, see Branch of a Phylogenetic Tree. 226
External Node, see Node of a Phylogenetic Tree. 226
Extrinsic Gene Prediction, see Gene Prediction, homology-based. 226
F 227
F-Measure 229
Concha Bielza and Pedro Larranaga 
229 
False Discovery Rate Control (False Discovery Rate, FDR) 229
John M. Hancock 229
False Discovery Rate in Proteomics 230
Simon Hubbard 230
Family-based Association Analysis 231
Mark McCarthy, Steven Wiltshire and Andrew Collins 231
FASTA (FASTP) 232
Jaap Heringa 232
FASTP, see FASTA. 234
FDR, see False Discovery Rate Control. 234
Feature (Independent Variable, Predictor Variable, Descriptor, Attribute, Observation) 234
Nello Cristianini 234
Feature Subset Selection 234
Pedro Larranaga 
234 
FGENES 236
Enrique Blanco and Josep F. Abril 236
FigTree 237
Michael P. Cummings 237
Fingerprint (Chemoinformatics), see Chemical Hashed Fingerprint. 237
Fingerprint of Proteins 237
Teresa K. Attwood 237
Finite Mixture Model 239
Pedro Larran˜ aga and Concha Bielza 239
Fisher Discriminant Analysis (Linear Discriminant Analysis) 239
Nello Cristianini 239
Flat File Data Formats 240
Carole Goble and Katy Wolstencroft 240
FLUCTUATE, see LAMARC. 241
Flux Balance Analysis, see Constraint-based Modeling. 241
Flybase 241
Guenter Stoesser and Dan Bolser 241
FLYBRAIN 242
Dan Bolser 242
Fold 243
Andrew Harrison, Alison Cuff and Christine Orengo 243
Fold Library 243
Andrew Harrison and Christine Orengo 243
Foldback, see RNA hairpin. 244
Folding Free Energy 244
Antonio Marco and Sam Griffiths-Jones 244
Founder Effect 245
A.R. Hoelzel 245
Frame-based Language 245
Robert Stevens 245
Free R-Factor 246
Liz Carpenter 246
Frequent Itemset, see Association Rule Mining. 246
Frequent Sub-Graph, see Graph Mining. 246
Frequent Sub-Structure, see Graph Mining. 246
Function Prediction, see Discrete Function Prediction. 246
Functional Database 247
Dov Greenbaum 247
Functional Genomics 247
Jean-Michel Claverie 247
Functional Signature 249
Jean-Michel Claverie 249
Functome 249
Dov Greenbaum 249
Fuzzy Logic, see Fuzzy Set. 250
Fuzzy Set (Fuzzy Logic, Possibility Theory) 250
Feng Chen and Yi-Ping Phoebe Chen 250
G 253
GA, see Genetic Algorithm. 255
Gametic Phase Disequilibrium, see Linkage Disequilibrium. 255
Gap 255
Jaap Heringa 255
Gap Penalty 255
Jaap Heringa and Laszlo Patthy 255
GARLI (Genetic Algorithm for Rapid Likelihood Inference) 256
Michael P. Cummings 256
Garnier-Osguthorpe-Robson Method, see GOR Secondary Structure Prediction Method. 257
GASP (Genome Annotation Assessment Project, E-GASP) 257
Enrique Blanco and Josep F. Abril 257
GBROWSE, see Gene Annotation, visualization tools 258
GC Composition, see Base Composition. 258
GC Richness, see Base Composition. 258
GEISHA 258
Dan Bolser 258
GenBank 259
Guenter Stoesser, Obi L. Griffith and Malachi Griffith 259
GENCODE 259
Enrique Blanco and Josep F. Abril 259
Gene Annotation 260
Enrique Blanco and Josep F. Abril 260
Gene Annotation, formats 261
Enrique Blanco and Josep F. Abril 261
Gene Annotation, hand-curated 262
Enrique Blanco and Josep F. Abril 262
Gene Annotation, visualization tools 263
Enrique Blanco and Josep F. Abril 263
Gene Cluster 264
Katheleen Gardiner 264
Gene Dispensability 264
Dov Greenbaum 264
Gene Distribution 265
Katheleen Gardiner 265
Gene Diversity 265
Mark McCarthy, Steven Wiltshire and Andrew Collins 265
Gene Duplication 266
Dov Greenbaum and Katheleen Gardiner 266
Gene Expression Database (GXD), see Mouse Genome Informatics. 267
Gene Expression Profile 267
Jean-Michel Claverie and John M. Hancock 267
Gene Family 268
Teresa K. Attwood and Katheleen Gardiner 268
Gene Finding, see Gene Prediction. 269
Gene-finding Format, see Gene Annotation, formats. 269
Gene Flow 269
A.R. Hoelzel 269
Gene Fusion Method 269
Patrick Aloy 269
Gene Index 270
Matthew He 270
Gene Neighbourhood 270
Patrick Aloy 270
Gene Ontology (GO) 271
Robert Stevens 271
Gene Ontology Consortium 271
Robert Stevens 271
Gene Prediction 271
Enrique Blanco, Josep F. Abril and Roderic Guigo 271
Gene Prediction, ab initio 273
Enrique Blanco, Josep F. Abril and Roderic Guigo 273
Gene Prediction, accuracy 277
Enrique Blanco, Josep F. Abril and Roderic Guigo 
277 
Gene Prediction, alternative splicing 279
Enrique Blanco and Josep F. Abril 279
Gene Prediction, comparative 280
Enrique Blanco, Josep F. Abril and Roderic Guigo 280
Gene Prediction, homology-based (Extrinsic Gene Prediction, Look-Up Gene Prediction) 282
Enrique Blanco, Josep F. Abril and Roderic Guigo 282
Gene Prediction, NGS-based 284
Enrique Blanco and Josep F. Abril 284
Gene Prediction, non-canonical 285
Enrique Blanco and Josep F. Abril 285
Gene Prediction, pipelines 286
Enrique Blanco, Josep F. Abril and Roderic Guigo 286
Gene Size 288
Katheleen Gardiner 288
Gene Symbol 288
John M. Hancock 288
Gene Symbol, human 289
Matthew He 289
Gene Transfer Format, see Gene Annotation, formats 289
Genealogical Sorting Index (gsi) 289
Michael P. Cummings 289
GeneChip, see Affymetrix GeneChipâ„¢ Oligonucleotide Microarray. 290
GENEID 290
Enrique Blanco and Josep F. Abril 290
General Feature Format, see Gene Annotation, Formats. 292
Generalization, see Error Measures. 292
Genetic Algorithm (GA) 292
Pedro Larranaga 
292 
Genetic Code (Universal Genetic Code, Standard Genetic Code) 293
J.M. Hancock 293
Genetic Linkage, see Linkage 294
Genetic Network 294
Denis Thieffry 294
Genetic Redundancy 295
Katheleen Gardiner 295
Genetic Variation, see Variation (Genetic). 295
GENEWISE 296
Roderic Guigo 296
Genome Annotation 296
Jean-Michel Claverie 296
Genome Annotation Assessment Project, see GASP. 298
Genome Scans for Linkage (Genome-Wide Scans) 298
Mark McCarthy, Steven Wiltshire and Andrew Collins 298
Genome Size (C-Value) 299
Katheleen Gardiner 299
Genome-Wide Association Study (GWAS) 299
Andrew Collins 299
Genome-Wide Scans (linkage), see Genome Scans 300
Genome-Wide Survey 300
Dov Greenbaum 300
GENOMEGRAPHS, see Gene Annotation, visualization tools. 301
Genomics 301
Stuart Brown 301
Genotype Imputation 302
Andrew Collins 302
GENSCAN 303
Enrique Blanco, Josep F. Abril and Roderic Guigo 303
GFF, see Gene Annotation, formats. 304
GFF2PS, see Gene Annotation, visualization tools. 304
GFF3, see Gene Annotation, formats. 304
Gibbs Sampling, see Markov Chain Monte Carlo. 304
Global Alignment 305
Jaap Heringa 305
Global Organisation for Bioinformatics Learning, Education & Training (GOBLET), see BTN.
Globular 305
Roman Laskowski and Tjaart de Beer 305
GO, see Gene Ontology. 306
GOBASE (Organelle Genome Database) 306
Guenter Stoesser, Obi L. Griffith and Malachi Griffith 306
GOBLET, see BTN. 306
GOBO, see Global Open Biology Ontologies. 306
GOR Secondary Structure Prediction Method (Garnier-Osguthorpe-Robson Method) 307
Patrick Aloy 307
Gradient Descent (Steepest Descent Method) 307
Nello Cristianini 307
GRAIL 308
Roderic Guigo 308
GRAIL Description Logic 309
Robert Stevens 309
Gramene 309
Dan Bolser 309
Graph Mining (Frequent Sub-Graph, Frequent Sub-Structure) 310
Feng Chen and Yi-Ping Phoebe Chen 310
Graph Representation of Genetic, Molecular and Metabolic Networks 310
Denis Thieffry 310
Group I Intron, see Intron. 312
Group II Intron, see Intron. 312
GTF, see Gene Annotation, formats. 312
Guilt by Association Annotation, see Annotation Transfer. 312
Gumball Machine 312
Thomas D. Schneider 312
GWAS, see Genome-Wide Association Study. 313
GWAS Central 313
Guenter Stoesser, Malachi Griffith and Obi L. Griffith 313
H 315
h2, see Heritability. 317
Hand-curated Gene Annotation, see Gene Annotation, hand-curated. 317
Haplotype 317
Mark McCarthy, Steven Wiltshire and Andrew Collins 317
HapMap Project 318
Andrew Collins 318
Hardy-Weinberg Equilibrium 319

319 
Haseman-Elston Regression (HE-SD, HE-SS, HE-CP and HE-COM) 320
Mark McCarthy and Steven Wiltshire 320
Hash, see Data Structure. 321
HAVANA (Human and Vertebrate Analysis and Annotation) 321
John M. Hancock 321
HE-COM, HE-CP, HE-SD, HE-SS, see Haseman-Elston Regression 321
Helical Wheel 321
Teresa K. Attwood 321
Heritability (h2, Degree of Genetic Determination) 323
Mark McCarthy, Steven Wiltshire and Andrew Collins 323
Heterotachy 324
Aidan Budd and Alexandros Stamatakis 324
HGMD (Human Gene Mutation Database) 324
Malachi Griffith and Obi L. Griffith 324
HGT, see Horizontal Gene Transfer. 325
HGVBASE, see GWAS Central. 325
Hidden Markov Model (HMM, Hidden Semi-Markov Models, Profile Hidden Markov Models, Training of Hidden Markov Models, Dynamic Programming, Pair Hidden Markov Models) 325
Irmtraud Meyer 325
Hierarchy 328
Robert Stevens 328
High-Scoring Segment Pair (HSP) 329
Jaap Heringa 329
HIV RT and Protease Sequence Database, see STanford HIV RT and Protease Sequence Database. 329
HIV Sequence Database 329
Guenter Stoesser, Malachi Griffith and Obi L. Griffith 329
HMM, see Hidden Markov Model. 330
HMMer 330
J.M. Hancock and M.J. Bishop 330
Homologous Genes 331
Austin L. Hughes and Laszlo Patthy 331
Homologous Superfamily 331
Andrew Harrison and Christine Orengo 331
Homology 332
Jaap Heringa and Laszlo Patthy 332
Homology Modeling, see Comparative Modeling. 333
Homology Search 333
Jaap Heringa 333
Homology-based Gene Prediction, see Gene Prediction, homology-based. 335
Homozygosity Mapping 335
Mark McCarthy, Steven Wiltshire and Andrew Collins 335
Horizontal Gene Transfer (HGT) 336
Dov Greenbaum 336
HSP, see High-scoring Segment Pair. 337
HTU, see Hypothetical Taxonomic Unit. 337
HUGO (The Human Genome Organization) 337
Pedro Fernandes 337
Human-Curated Gene Annotation, see Gene Annotation, hand-curated. 338
Human Gene Mutation Database, see HGMD. 338
Human Genome Variation Database, see HGVBASE. 338
Human Proteome Organization, see HUPO. 338
Human Variome Project (HVP) 339
John M. Hancock 339
HUPO (Human Proteome Organization) 339
Pedro Fernandes 339
HVP, see Human Variome Project. 340
Hydrogen Bond 340
Jeremy Baum 340
Hydropathy 340
Teresa K. Attwood 340
Hydropathy Profile (Hydrophobicity Plot, Hydrophobic Plot) 342
Teresa K. Attwood 342
Hydrophilicity 343
Jeremy Baum 343
Hydrophobic Moment 343
Jeremy Baum 343
Hydrophobic Scale 344
Jeremy Baum 344
Hydrophobicity Plot, see Hydropathy Profile. 344
HyPhy (Hypothesis Testing Using Phylogenies) 344
Michael P. Cummings 344
Hypothetical Taxonomic Unit (HTU) 344
Aidan Budd and Alexandros Stamatakis 344
I 345
IBD, see Identical by Descent. 347
IBS, see Identical by State. 347
IC50, see Binding Affinity. 347
ICA, see Independent Component Analysis. 347
Identical by Descent (Identity by Descent, IBD) 347
Mark McCarthy and Steven Wiltshire 347
Identical by State (Identity by State, IBS) 348
Mark McCarthy and Steven Wiltshire 348
IGV, see Gene Annotation, visualization tools. 348
IMa2 (Isolation with Migration a2) 348
Michael P. Cummings 348
IMGT (International Immunogenetics Database) 349
Guenter Stoesser, Malachi Griffith and Obi L. Griffith 349
Imprinting 349
Mark McCarthy, Steven Wiltshire and Andrew Collins 349
Imputation, see Genotype Imputation. 350
InChI (International Chemical Identifier) 350
Bissan Al-Lazikani 350
InChi Key 351
Bissan Al-Lazikani 351
Indel (Insertion-Deletion Region, Insertion, Deletion, Gap) 351
Teresa K. Attwood 351
Independent Component Analysis (ICA) 352
Concha Bielza and Pedro Larranaga 
352 
Independent Variables, see Features. 353
Individual (Instance) 353
Robert Stevens 353
Individual Information 353
Thomas D. Schneider 353
Information 354
Thomas D. Schneider 354
Information Retrieval, see Text Mining. 354
Information Theory 354
Thomas D. Schneider 354
Initiator Sequence 355
Niall Dillon 355
INPPO (International Plant Proteomics Organization) 355
Pedro Fernandes 355
Insertion, Insertion-Deletion Region, see Indel. 356
Instance, see Individual. 356
Instance-based Learner, see K-Nearest Neighbor Classification. 356
Integrated Gene Annotation Pipelines, see Gene Prediction, Pipelines. 356
Integrated Gene Prediction Systems, see Gene Prediction Systems, Pipelines. 356
Intelligent Data Analysis, see Pattern Analysis. 356
Interactome 356
Dov Greenbaum 356
Intergenic Sequence 357
Katheleen Gardiner 357
Interior Branch, Internal Branch, see Branch and Phylogenetic Tree. 358
Interior Node, Internal Node, see Node and Phylogenetic Tree. 358
International Chemical Identifier, see InChi. 358
International Immunogenetics Database, see IMGT. 358
International Plant Proteomics Organization, see INPPO. 358
International Society for Computational Biology (ISCB) 358
Pedro Fernandes 358
Interolog (Interologue) 359
Dov Greenbaum 359
InterPro 359
Teresa K. Attwood 359
InterProScan, see InterPro. 361
Interspersed Sequence (Long-Term Interspersion, Long-Period Interspersion, Short-Term Interspersion, Short-Period Interspersion, Locus Repeat) 361
Dov Greenbaum 361
Intrinsic Gene Prediction, see Gene Prediction, ab initio. 361
Intron 362
Niall Dillon and John M. Hancock 362
Intron Phase 362
Austin L. Hughes 362
IR, see Text Mining. 363
ISCB, see International Society for Computational Biology. 363
Isobaric Tagging 363
Simon Hubbard 363
Isochore 363
Katheleen Gardiner 363
IsomiR 364
Ana Kozomara and Sam Griffiths-Jones 364
Iteration 364
Matthew He 364
IUPAC-IUB Codes (Nucleotide Base Codes, Amino Acid Abbreviations) 364
John M. Hancock 364
J 367
Jaccard Distance ( Jaccard Index, Jaccard Similarity Coefficient) 369
John M. Hancock 369
Jackknife 369
Dov Greenbaum 369
JASPAR 369
Obi L. Griffith and Malachi Griffith 369
JELLYFISH 370
Michael P. Cummings 370
jModelTest 370
Michael P. Cummings 370
Jpred, see Web-based Secondary Structure Prediction Programs. 371
Jumping Gene, see Transposable Element. 371
Junk DNA 371
Dov Greenbaum 371
K 373
K-Fold Cross-Validation, see Cross-Validation. 375
K-Means Clustering, see Clustering. 375
K-Medoids 375
Concha Bielza and Pedro Larranaga 
375 
K-Nearest Neighbor Classification (Lazy Learner, KNN, Instance-based Learner) 375
Feng Chen and Yi-Ping Phoebe Chen 375
Kappa Virtual Dihedral Angle 376
Roman Laskowski and Tjaart de Beer 376
Karyotype 376
Katheleen Gardiner 376
Kd, see Binding Affinity. 377
Kernel-based Learning Method, see Kernel Method. 377
Nello Cristianini 377
Kernel Machine, see Kernel Method. 378
Kernel Method (Kernel Machine, Kernel-based Learning Method) 378
Nello Cristianini 378
Ki, see Binding Affinity. 379
KIF, see Knowledge Interchange Format. 379
Kin Selection 379
A.R. Hoelzel 379
Kinetic Modeling 380
Neil Swainston 380
Kinetochore 381
Katheleen Gardiner 381
Kingdom 381
Dov Greenbaum 381
KNN, see K-Nearest Neighbor Classification, Lazy Learner, Instance-based Learner. 382
Knowledge 382
Robert Stevens 382
Knowledge Base 383
Robert Stevens 383
Knowledge-based Modeling, see Homology Modeling. 383
Knowledge Interchange Format (KIF) 383
Robert Stevens 383
Knowledge Map, see Bayesian Network. 384
Robert Stevens 384
Kozak Sequence 386
Niall Dillon 386
KRL, see Knowledge Representation Language. 386
L 387
L-G Algorithm, see Lander-Green Algorithm. 389
Label (Labeled Data, Response, Dependent Variable) 389
Nello Cristianini 389
Labeled Data, see Label. 389
Labeled Tree 389
Aidan Budd and Alexandros Stamatakis 389
Laboratory Information Management System (LIMS) 390
John M. Hancock 390
LAMARC 390
Michael P. Cummings 390
Lander-Green Algorithm (L-G Algorithm) 391
Mark McCarthy, Steven Wiltshire and Andrew Collins 391
Lattice 392
Robert Stevens 392
Lazy Learner, see K-Nearest Neighbor Classification. 393
LD, see Linkage Disequilibrium. 393
Lead Optimization 393
Matthew He 393
Leaf, see Node and Phylogenetic Tree. 393
Leave-One-Out Validation, see Cross-Validation. 393
Leiden Open Variation Database, see Locus-Specific Database. 393
Lexicon 393
Robert Stevens 393
Ligand Efficiency 394
Bissan Al-Lazikani 394
LIMS, see Laboratory Information Management System. 394
LINE (Long Interspersed Nuclear Element) 394
Dov Greenbaum 394
Linear Discriminant Analysis, see Fisher Discriminant Analysis. 395
Linear Regression and Non-Linear Regression, see Regression Analysis. 395
Linkage (Genetic Linkage) 395
Mark McCarthy and Steven Wiltshire 395
Linkage Analysis 396
Mark McCarthy, Steven Wiltshire and Andrew Collins 396
Linkage Disequilibrium (LD, Gametic Phase Disequilibrium, Allelic Association) 397
Mark McCarthy, Steven Wiltshire and Andrew Collins 397
Linkage Disequilibrium Analysis, see Association Analysis. 399
Linkage Disequilibrium Map 399
Andrew Collins 399
Linked Data 400
Carole Goble and Katy Wolstencroft 400
Linked List, see Data Structure. 401
Lipinski Rule of Five, see Rule of Five. 401
Local Alignment (Local Similarity) 401
Jaap Heringa 401
Local Similarity, see Local Alignment. 402
Locus Repeat, see Interspersed Sequence. 402
Locus-Specific Database (Locus-Specific Mutation Database, LSDB) 402
John M. Hancock 402
LOD Score (Logarithm of Odds Score) 402
Mark McCarthy, Steven Wiltshire and Andrew Collins 402
Log Odds Score, see Amino Acid Exchange Matrix, LOD Score. 404
LogDet, see Paralinear Distance. 404
Logical Modeling of Genetic Networks 404
Denis Thieffry 404
Logo, see Sequence Logo. 405
LogP (ALogP, CLogP) 406
Bissan Al-Lazikani 406
Long-Period Interspersion, see Interspersed Sequence. 406
Long-Term Interspersion, see Interspersed Sequence. 406
Look-Up Gene Prediction, see Gene Prediction, Homology-based. 406
Loop 406
Marketa J. Zvelebil 406
Loop Prediction/Modeling 407
Roland Dunbrack 407
LOVD, see Locus-Specific Database. 408
Low Complexity Region 408
Jaap Heringa and Patrick Aloy 408
LSDB, see Locus-Specific Database. 408
M 409
MacClade 413
Michael P. Cummings 413
Machine Learning 413
Nello Cristianini 413
Majority-Rule Consensus Tree, see Consensus Tree. 414
Mammalian Gene Collection, see MGC. 414
Mammalian Promoter Database, see MpromDB. 414
Manual Gene Annotation, see Gene Annotation (hand-curated). 414
Map Function 414
Mark McCarthy and Steven Wiltshire 414
Mapping by Admixture Linkage Disequilibrium, see Admixture Mapping. 416
Mark-up Language 416
Carole Goble and Katy Wolstencroft 416
Marker 416
Mark McCarthy, Steven Wiltshire and Andrew Collins 416
Markov Chain 417
John M. Hancock 417
Markov Chain Monte Carlo (MCMC, Metropolis-Hastings, Gibbs Sampling) 418
John M. Hancock 418
Markov Model, see Hidden Markov Model, Markov Chain. 418
Mathematical Modeling (of Molecular/Metabolic/Genetic Networks) 419
Denis Thieffry 419
Mature microRNA 422
Sam Griffiths-Jones 422
Maximal Margin Classifier, see Support Vector Machine. 422
Maximum Likelihood Phylogeny Reconstruction 422
Sudhir Kumar and Alan Filipski 422
Maximum Parsimony Principle (Parsimony, Occam's 
423 
Sudhir Kumar, Alan Filipski and Dov Greenbaum 423
MaxQuant 424
Simon Hubbard 424
MCMC, see Markov Chain Monte Carlo. 425
MEGA (Molecular Evolutionary Genetics Analysis) 425
Michael P. Cummings 425
Mendelian Disease 425
Mark McCarthy, Steven Wiltshire and Andrew Collins 425
MEROPS 426
Rolf Apweiler 426
Mesquite 427
Michael P. Cummings 427
Message 427
Thomas D. Schneider 427
Metabolic Modeling 428
Neil Swainston 428
Metabolic Network 428
Neil Swainston 428
Metabolic Pathway 429
Neil Swainston 429
Metabolome (Metabonome) 429
Dov Greenbaum 429
Metabolomics Databases 430
Darren Creek 430
Metabolomics Software 431
Richard Scheltema 431
Metabonome, see Metabolome. 433
Metadata 433
Robert Stevens 433
Metropolis-Hastings, see Markov Chain Monte Carlo. 434
MGC (Mammalian Gene Collection) 434
Malachi Griffith and Obi L. Griffith 434
MGD (Mouse Genome Database) 434
Guenter Stoesser 434
MGED Ontology 435
Robert Stevens 435
Microarray 436
Stuart Brown 436
Microarray Image Analysis 437
Stuart Brown 437
Microarray Normalization 437
Stuart Brown 437
Microfunctionalization 439
John M. Hancock 439
MicroRNA 439
Sam Griffiths-Jones 439
MicroRNA Discovery 440
Antonio Marco and Sam Griffiths-Jones 440
MicroRNA Family 441
Antonio Marco and Sam Griffiths-Jones 441
MicroRNA Prediction, see MicroRNA Discovery. 442
MicroRNA Seed 442
Ana Kozomara and Sam Griffiths-Jones 442
MicroRNA Seed Family, see MicroRNA Family. 442
MicroRNA Target 442
Antonio Marco and Sam Griffiths-Jones 442
MicroRNA Target Prediction 443
Antonio Marco and Sam Griffiths-Jones 443
Microsatellite 444
Katheleen Gardiner 444
Midnight Zone 445
Teresa K. Attwood 445
MIGRATE-N 446
Michael P. Cummings 446
MIME Types 447
Eric Martz 447
Minimum Evolution Principle 448
Sudhir Kumar and Alan Filipski 448
Minimum Information Models 449
Carole Goble and Katy Wolstencroft 449
Minisatellite 450
Katheleen Gardiner 450
miRBase 450
Ana Kozomara and Sam Griffiths-Jones 450
Mirtron 451
Antonio Marco and Sam Griffiths-Jones 451
Missing Data, see Missing Value. 451
Missing Value (Missing Data) 451
Feng Chen and Yi-Ping Phoebe Chen 451
Mitelman Database (Chromosome Aberrations and Gene Fusions in Cancer) 452
Malachi Griffith and Obi L. Griffith 452
Mixture Models 453
Aidan Budd and Alexandros Stamatakis 453
MM, see Markov Chain. 453
MOD, see Model Organism Database. 453
Model Order Selection, see Model Selection. 454
Model Organism Database (MOD) 454
Obi L. Griffith and Malachi Griffith 454
Model Selection (Model Order Selection, Complexity Regularization) 454
Nello Cristianini 454
Modeling, Macromolecular 455
Eric Martz 455
Models, Molecular 456
Eric Martz 456
Modeltest 458
Michael P. Cummings 458
ModENCODE, see ENCODE. 459
Modular Protein 459
Laszlo Patthy 459
Module Shuffling 459
Laszlo Patthy 459
Mol Chemical Representation Format 459
Bissan Al-Lazikani 459
Molecular Clock (Evolutionary Clock, Rate of Evolution) 460
Sudhir Kumar and Alan Filipski 460
Molecular Coevolution, see Coevolution. 461
Molecular Drive, see Concerted Evolution. 461
Molecular Dynamics Simulation 461
Roland Dunbrack 461
Molecular Efficiency 462
Thomas D. Schneider 462
Molecular Evolutionary Mechanisms 463
Dov Greenbaum 463
Molecular Information Theory 464
Thomas D. Schneider 464
Molecular Machine 465
Thomas D. Schneider 465
Molecular Machine Capacity 465
Thomas D. Schneider 465
Molecular Machine Operation 466
Thomas D. Schneider 466
Molecular Mechanics 466
Roland Dunbrack 466
MOLECULAR NETWORK, see Network. 467
Molecular Replacement 467
Liz Carpenter 467
Monophyletic Group, see Clade. 468
Monte Carlo Simulation 468
Roland Dunbrack 468
Motif 469
Teresa K. Attwood and Dov Greenbaum 469
Motif Discovery 470
Jacques van Helden 470
Motif Enrichment Analysis 471
Jacques van Helden 471
Motif Search 472
Jaap Heringa 472
Mouse Genome Database, see Mouse Genome Informatics. 477
Mouse Genome Informatics (MGI, Mouse Genome Database, MGD) 477
Dan Bolser 477
Mouse Tumor Biology (MTB) Database, see Mouse Genome Informatics. 477
MouseCyc, see Mouse Genome Informatics. 477
MPromDB (Mammalian Promoter Database) 477
Obi L. Griffith and Malachi Griffith 477
MrBayes 478
Michael P. Cummings 478
Multidomain Protein 479
Laszlo Patthy 479
Multifactorial Trait (Complex Trait) 479
Mark McCarthy and Steven Wiltshire 479
Multifurcation (Polytomy) 480
Aidan Budd and Alexandros Stamatakis 480
Multilabel Classification 480
Concha Bielza and Pedro Larranaga 
480 
Multilayer Perceptron, see Neural Network. 481
Multiple Alignment 481
Jaap Heringa 481
MULTIPLE HIERARCHY (Polyhierarchy) 485
Robert Stevens 485
Multiplex Sequencing 485
Matthew He 485
Multipoint Linkage Analysis 485
Mark McCarthy and Steven Wiltshire 485
Murcko Framework, see Bemis and Murcko Framework. 486
Mutation Matrix, see Amino Acid Exchange Matrix. 486
N 487
N-terminus (amino terminus) 489
Roman Laskowski and Tjaart de Beer 489
Naiv 
489 
National Center for Biotechnology Information, see NCBI. 489
Natural Selection 489
A.R. Hoelzel 489
NCBI (National Center for Biotechnology Information) 490
Guenter Stoesser, Malachi Griffith and Obi L. Griffith 490
NDB, see Nucleic Acid Database. 491
Nearest Neighbor Methods 491
Patrick Aloy 491
Nearly Neutral Theory, see Neutral Theory. 491
Needleman-Wunsch Algorithm 491
Jaap Heringa 491
Negative Selection, see Purifying Selection. 492
Negentropy (Negative Entropy) 492
Thomas D. Schneider 492
Neighbor-Joining Method 492
Sudhir Kumar and Alan Filipski 492
Network (Genetic Network, Molecular Network, Metabolic Network) 493
Denis Thieffry 493
Neural Network (Artificial Neural Network, Connectionist Network, Backpropagation Network, Multilayer Perceptron) 496
Nello Cristianini 496
Neutral Theory (Nearly Neutral Theory) 498
A.R. Hoelzel 498
Newton-Raphson Minimization, see Energy Minimization. 498
Next Generation DNA Sequencing 499
Stuart Brown 499
Next Generation Sequencing, De Novo Assembly, see De Novo Assembly in Next Generation Sequencing. 500
Nit 500
Thomas D. Schneider 500
NMR (Nuclear Magnetic Resonance) 501
Liz Carpenter 501
Node, see Phylogenetic Tree. 502
Noise (Noisy Data) 502
Thomas D. Schneider 502
Non-Crystallographic Symmetry, see Space Group. 502
Non-Parametric Linkage Analysis, see Allele-Sharing Methods. 502
Non-Synonymous Mutation 502
Laszlo Patthy 502
NOR, see Nucleolar Organizer Region. 502
NoSQL, see Database. 502
Nuclear Intron, see Intron. 502
Nuclear Magnetic Resonance, see NMR. 502
Nucleic Acid Database (NDB) 503
Guenter Stoesser 503
Nucleic Acid Sequence Databases 503
Guenter Stoesser 503
Nucleolar Organizer Region (NOR) 504
Katheleen Gardiner 504
Nucleotide Base Codes, See IUPAC-IUB Codes. 504
O 505
OBF (The Open Bioinformatics Foundation) 507
Pedro Fernandes 507
Object, see Data Structure. 507
Object-Relational Database 507
Matthew He 507
OBO-Edit 508
John M. Hancock 508
OBO Foundry 508
John M. Hancock 508
Observation, see Feature. 508
Occam's 
508 
ODB (Operon DataBase) 509
Obi L. Griffith and Malachi Griffith 509
Offspring Branch (Daughter Branch/Lineage) 509
Aidan Budd and Alexandros Stamatakis 509
OKBS, see Open Knowledge Base Connectivity. 509
Oligo Selection Program, see OSP. 509
Oligogenic Effect, see Oligogenic Inheritance. 509
Oligogenic Inheritance (Oligogenic Effect) 510
Mark McCarthy and Steven Wiltshire 510
Omics 510
John M. Hancock 510
OMIM (Online Mendelian Inheritance in Man) 511
Obi L. Griffith and Malachi Griffith 511
Online Mendelian Inheritance in Man, see OMIM. 511
Ontology 511
Robert Stevens 511
Open Biological and Biomedical Ontologies, see OBO Foundry. 512
Open Reading Frame (ORF) 512
Niall Dillon 512
Open Reading Frame Finder, see ORF Finder. 512
Open Regulatory Annotation Database, see OregAnno. 512
Operon DataBase, see OPD. 512
Open Source Bioinformatics Organizations 512
John M. Hancock 512
Operating System 513
Steve Pettifer, James Marsh and David Thorne 513
Operational Taxonomic Unit (OTU) 514
John M. Hancock 514
OPLS 514
Roland Dunbrack 514
Optimal Alignment 515
Jaap Heringa 515
Oral Bioavailability 515
Bissan Al-Lazikani 515
ORF, see Open Reading Frame. 515
ORegAnno (Open Regulatory Annotation Database) 515
Obi L. Griffith and Malachi Griffith 515
ORFan, see Orphan Gene. 516
Organelle Genome Database, see GOBASE. 516
Organism-Specific Database, see MOD. 516
Organismal Classification, see Taxonomic Classification. 516
Orphan Gene (ORFan) 517
Jean-Michel Claverie 517
Ortholog (Orthologue) 517
Dov Greenbaum 517
Outlier, see Outlier Mining. 518
Outlier Mining (Outlier) 518
Feng Chen and Yi-Ping Phoebe Chen 518
Overdominance 519
A.R. Hoelzel 519
Overfitting (Overtraining) 520
Nello Cristianini 520
Overtraining, see Overfitting. 520
OWL, see Web Ontology Language. 520
P 521
Pairwise Alignment 525
Jaap Heringa 525
PAM Matrix (of Amino Acid Substitutions), see Dayhoff Amino Acid Substitution Matrix, Amino Acid Exchange Matrix. 526
PAM Matrix of Nucleotide Substitutions (Point Accepted Mutations) 526
Laszlo Patthy 526
PAML (Phylogenetic Analysis by Maximum Likelihood) 526
Michael P. Cummings 526
Paralinear Distance (LogDet) 527
Dov Greenbaum 527
Parallel Computing in Phylogenetics 528
Aidan Budd and Alexandros Stamatakis 528
Paralog (Paralogue) 528
Austin L. Hughes, Dov Greenbaum and Laszlo Patthy 528
Parameter 529
Matthew He 529
Parametric Bootstrapping, see Bootstrapping. 529
Paraphyletic Group, see Cladistics. 530
Parent, see Template. 530
Parity Bit 530
Thomas D. Schneider 530
Parsimony 530
Dov Greenbaum 530
Partition Coefficient, see LogP. 531
Pattern 531
Matthew He 531
Pattern Analysis 532
Nello Cristianini 532
Pattern Discovery, see Motif Discovery. 532
Pattern of Change Analysis, see Phylogenetic Events Analysis. 532
Pattern Recognition, see Pattern Analysis. 532
PAUP* (Phylogenetic Analysis Using Parsimony (and Other Methods)) 532
Michael P. Cummings 532
PAZAR 533
Obi L. Griffith and Malachi Griffith 533
Pearson Correlation, see Regression Analysis. 533
Penalty, see Gap Penalty. 533
Penetrance 534
Mark McCarthy and Steven Wiltshire 534
Peptide 534
Roman Laskowski and Tjaart de Beer 534
Peptide Bond (Amide Bond) 535
Roman Laskowski and Tjaart de Beer 535
Peptide Mass Fingerprint 535
Simon Hubbard 535
Peptide Spectrum Match (PSM) 535
Simon Hubbard 535
PeptideAtlas 535
Simon Hubbard 535
Percent Accepted Mutation Matrix, see Dayhoff Amino Acid Substitution Matrix. 536
Petri Net 536
Anton Feenstra 536
Pfam 537
Teresa K. Attwood 537
PFM, see Position-Frequency Matrix. 537
Phantom Indel (Frame Shift) 538
Jaap Heringa 538
Pharmacophore 538
Bissan Al-Lazikani 538
Phase (Sensu Linkage) 538
Mark McCarthy and Steven Wiltshire 538
PheGenI, see dbGAP. 539
PHRAP 540
Rodger Staden 540
PHRED 540
Rodger Staden 540
PHYLIP (PHYLogeny Inference Package) 540
Michael P. Cummings 540
Phylogenetic Events Analysis (Pattern of Change Analysis) 541
Jamie J. Cannone and Robin R. Gutell 541
Phylogenetic Footprint 543
Jacques van Helden 543
Phylogenetic Footprint Detection 544
Jacques van Helden 544
Phylogenetic Placement of Short Reads 545
Aidan Budd, Erick Matsen and Alexandros Stamatakis 545
Phylogenetic Profile 545
Patrick Aloy 545
Phylogenetic Reconstruction, see Phylogenetic Tree. 546
Phylogenetic Shadowing, see Phylogenetic Footprinting. 546
Phylogenetic Tree (Phylogeny, Phylogeny Reconstruction, Phylogenetic Reconstruction) 546
Jaap Heringa 546
Phylogenetic Trees, Distance, see Distances Between Trees. 551
Phylogenetics 552
Aidan Budd and Alexandros Stamatakis 552
Phylogenomics 552
Jean-Michel Claverie 552
Phylogeny, Phylogeny Reconstruction, see Phylogenetic Tree. 553
Piecewise-Linear Models 553
Luis Mendoza 553
PIPMAKER 554
John M. Hancock 554
PlantsDB 554
Dan Bolser 554
Plesiomorphy 555
A.R. Hoelzel 555
Point Accepted Mutations, see PAM Matrix of Nucleotide Substitutions. 555
Polar 556
Roman Laskowski and Tjaart de Beer 556
Polarization 556
Roland Dunbrack 556
Polygenic Effect, see Polygenic Inheritance. 556
Polygenic Inheritance (Polygenic Effect) 556
Mark McCarthy and Steven Wiltshire 556
Polymorphism (Genetic Polymorphism) 557
Mark McCarthy and Steven Wiltshire 557
Polypeptide 558
Roman Laskowski and Tjaart de Beer 558
Polyphyletic Group, see Cladistics. 558
Polytomy, see Multifurcation. 558
PomBase 558
Dan Bolser 558
Population Bottleneck (Bottleneck) 559
A.R. Hoelzel 559
Position-Specific Scoring Matrix, see Profile. 559
Position Weight Matrix 560
Jacques van Helden 560
Position Weight Matrix of Transcription Factor Binding Sites 560
James Fickett 560
Positional Candidate Approach 561
Mark McCarthy and Steven Wiltshire 561
Positive Classification 562
Pedro Larran 
562 
Positive Darwinian Selection (Positive Selection) 563
Austin L. Hughes 563
Positive Selection, see Positive Darwinian Selection. 564
Post-Order Tree Traversal, see Tree Traversal. 564
Posterior Error Probability (PEP) 564
Simon Hubbard 564
Potential of Mean Force 564
Roland Dunbrack 564
Power Law (Zipf' 
565 
Dov Greenbaum 565
Prediction of Gene Function 565
Jean-Michel Claverie 565
Predictive ADME (Absorption, Distribution, Metabolism, and Excretion), see Chemoinformatics. 567
PRIDE 567
Simon Hubbard 567
PRIMER3 567
John M. Hancock 567
Principal Components Analysis (PCA) 568
John M. Hancock 568
PRINTS 568
Teresa K. Attwood 568
Probabilistic Network, see Bayesian Network. 570
ProDom 570
Teresa K. Attwood 570
Profile (Weight Matrix, Position Weight Matrix, Position-Specific Scoring Matrix, PSSM) 570
Teresa K. Attwood 570
Profile, 3D 571
Andrew Harrison and Christine Orengo 571
Profile Searching 572
Jaap Heringa 572
Programming and Scripting Languages 575
David Thorne, Steve Pettifer and James Marsh 575
Promoter 575
Niall Dillon 575
The Promoter Database of Saccharomyces cerevisiae (SCPD) 576
Dan Bolser 576
Promoter Prediction 576
James Fickett 576
PROSITE 577
Teresa K. Attwood 577
Protege 
578 
Robert Stevens and John M. Hancock 578
Protein Array (Protein Microarray) 579
Jean-Michel Claverie 579
Protein Data Bank (PDB) 579
Eric Martz 579
Protein Databases 581
Rolf Apweiler 581
Protein Domain 581
Laszlo Patthy 581
Protein Family 582
Andrew Harrison, Christine Orengo, Dov Greenbaum, and Laszlo Patthy 582
Protein Family and Domain Signature Databases 583
Rolf Apweiler 583
Protein Fingerprint, see Fingerprint. 583
Protein Inference Problem 584
Simon Hubbard 584
Protein Information Resource (PIR) 584
Rolf Apweiler 584
Protein Microarray, see Protein Array. 584
Protein Module 585
Laszlo Patthy 585
Protein-Protein Coevolution 585
Laszlo Patthy 585
Protein-Protein Interaction Network Inference 586
Hedi Peterson 586
Protein Sequence, see Sequence of Protein. 586
Protein Sequence Cluster Databases 587
Rolf Apweiler 587
Protein Structure 587
Roman Laskowski, Andrew Harrison, Christine Orengo and Tjaart AP de Beer 587
Protein Structure Classification Databases, see Structure 3D Classification. 588
Proteome 588
Dov Greenbaum 588
Proteome Analysis Database (Integr8) 589
Marketa J. Zvelebil 589
Proteomics 590
Jean-Michel Claverie 590
Proteomics Standards Initiative (PSI) 591
Simon Hubbard 591
Proteotypic Peptide 591
Simon Hubbard 591
Pseudoparalog (pseudoparalogue) 592
Laszlo Patthy 592
Pseudogene 592
Dov Greenbaum 592
PSI BLAST 593
Dov Greenbaum 593
PSSM, see Profile. 594
Purifying Selection (Negative Selection) 594
Austin L. Hughes 594
Q 597
Qindex (Qhelix Qstrand
Patrick Aloy 599
QM/MM Simulations 599
Roland Dunbrack 599
QSAR (Quantitative Structure Activity Relationship) 599
Marketa J. Zvelebil and Bissan Al-Lazikani 599
Qualitative and Quantitative Databases used in Systems Biology 600
Pascal Kahlem 600
Qualitative Differential Equations 601
Luis Mendoza 601
Quantitative Proteomics 602
Simon Hubbard 602
Quantitative Trait (Continuous Trait) 602

602 
Quartets, Phylogenetic 604
Sudhir Kumar and Alan Filipski 
604 
Quartet Puzzling, see Quartet, Phylogenetic. 604
Quaternary Structure 605
Roman Laskowski and Tjaart de Beer 
605 
R 607
R-Factor 609
Liz Carpenter 
609 
r8s 609
Michael P. Cummings 
609 
Ramachandran Plot 610
Roman Laskowski and Tjaart de Beer 
610 
Random Forest 611
Concha Bielza and Pedro Larran 
611 
Random Trees 611
Concha Bielza and Pedro Larran 
611 
Rat Genome Database (RGD) 612
Guenter Stoesser 
612 
Rate Heterogeneity 612
Aidan Budd and Alexandros Stamatakis 
612 
Rational Drug Design, see Structure-based Drug Design. 613
RDF 613
Carole Goble and Katy Wolstencroft 
613 
RDF Database, see Database. 614
readseq 614
Michael P. Cummings 
614 
Reasoning 614
Robert Stevens 
614 
Recombination 614
Mark McCarthy and Steven Wiltshire 614
RECOMBINE, see LAMARC. 615
Record, see Data Structure. 615
Recursion 616
Matthew He 
616 
Reference Genome (Type Genome) 616
John M. Hancock 
616 
Reference Sequence Database, see RefSeq. 616
Refinement 616
Liz Carpenter 
616 
RefSeq (the Reference Sequence Database) 617
Malachi Griffith and Obi L. Griffith 
617 
Regex, see Regular Expresssion. 618
Regression Analysis 618
Nello Cristianini 
618 
Regression Tree 618
Concha Bielza and Pedro Larran 
618 
Regular Expression (Regex) 619
Teresa K. Attwood 
619 
Regularization (Ridge, Lasso, Elastic Net, Fused Lasso, Group Lasso) 620
Concha Bielza and Pedro Larran 
620 
Regulatory Motifs in Network Biology 621
Denis Thieffry 
621 
Regulatory Network Inference 622
Hedi Peterson 
622 
Regulatory Region 623
Jacques van Helden 
623 
Regulatory Region Prediction 623
James Fickett 
623 
Regulatory Sequence, see Transcriptional Regulatory Region. 625
Regulome 625
John M. Hancock 
625 
Relational Database 625
Feng Chen and Yi-Ping Phoebe Chen 
625 
Relational Database Management System (RDBMS) 625
Matthew He 
625 
Relationship 625
Robert Stevens 
625 
REPEATMASKER 626
John M. Hancock 
626 
Repeats Alignment, see Alignment. 626
Repetitive Sequences, see Simple DNA Sequence. 627
Residue, see Amino Acid. 627
Resolution in X-Ray Crystallography 627
Liz Carpenter 
627 
Response, see Label. 628
RESTful Web Services 628
Carole Goble and Katy Wolstencroft 
628 
Restriction Map 628
Matthew He 
628 
Retrosequence 628
Austin L. Hughes 
628 
Retrotransposon 629
Dov Greenbaum 
629 
Reverse Complement 629
John M. Hancock 
629 
Rfam 630
Sam Griffiths-Jones 
630 
Rfrequency 630
Thomas D. Schneider 
630 
RGD, see Rat Genome Database. 631
Ri 631
Thomas D. Schneider 
631 
Ribosomal RNA (rRNA) 631
Robin R. Gutell 
631 
Ribosome Binding Site (RBS) 636
John M. Hancock 
636 
RMSD, see Root Mean Square Deviation. 636
RNA (General Categories) 637
Robin R. Gutell 
637 
RNA Folding 640
Jamie J. Cannone and Robin R. Gutell 
640 
RNA Hairpin 640
Antonio Marco and Sam Griffiths-Jones 
640 
RNA-seq 641
Stuart Brown 
641 
RNA Splicing, see Splicing. 642
RNA Structure 642
Jamie J. Cannone and Robin R. Gutell 
642 
RNA Structure Prediction (Comparative Sequence Analysis) 645
Jamie J. Cannone and Robin R. Gutell 
645 
RNA Structure Prediction (Energy Minimization) 646
Jamie J. Cannone and Robin R. Gutell 
646 
RNA Tertiary Structure Motifs 647
Jamie J. Cannone and Robin R. Gutell 
647 
Robustness 651
Dov Greenbaum and Marketa J. Zvelebil 
651 
ROC Curve 652
Pedro Larran 
652 
Role 653
Robert Stevens 
653 
Root Mean Square Deviation (RMSD) 653
Roman Laskowski and Tjaart de Beer 
653 
Rooted Phylogenetic Tree, see Phylogenetic Tree. Contrast with Unrooted Phylogenetic Tree. 654
Rooting Phylogenetic Trees 654
Sudhir Kumar and Alan Filipski 
654 
Rosetta Stone Method 655
Jean-Michel Claverie 
655 
Rotamer 656
Roland Dunbrack 
656 
Rough Set 656
Feng Chen and Yi-Ping Phoebe Chen 
656 
rRNA, see Ribosomal RNA. 657
Rsequence 657
Thomas D. Schneider 
657 
Rule 658
Teresa K. Attwood 
658 
Rule Induction 658
Pedro Larran 
658 
Rule of Five (Lipinski Rule of Five) 659
Bissan Al-Lazikani 
659 
S 661
Saccharomyces Genome Database, see SGD. 665
Safe Zone 665
Patrick Aloy 
665 
SAGE (Serial Analysis of Gene Expression) 665
Jean-Michel Claverie 
665 
SAR (Structure– 
666 
Bissan Al-Lazikani 
666 
Scaffold 666
Bissan Al-Lazikani 
666 
Scaled Phylogenetic Tree, see Branch. Contrast with Unscaled Phylogenetic Tree. 667
Schematic (Ribbon, Cartoon) Models 667
Eric Martz 
667 
Scientific Workflows 667
Carole Goble and Katy Wolstencroft 
667 
Score 668
Thomas D. Schneider 
668 
Scoring Matrix (Substitution Matrix) 668
Teresa K. Attwood 
668 
SCWRL 670
Roland Dunbrack 
670 
SDF 671
Bissan Al-Lazikani 
671 
Search by Signal, see Sequence Motifs: prediction and modeling. 671
Second Law of Thermodynamics 671
Thomas D. Schneider 
671 
Secondary Structure of Protein 672
Roman Laskowski and Tjaart de Beer 
672 
Secondary Structure Prediction of Protein 672
Patrick Aloy 
672 
Secretome 673
Dov Greenbaum 
673 
Segmental Duplication 674
Dov Greenbaum 
674 
Segregation Analysis 675
Mark McCarthy and Steven Wiltshire 
675 
Selected Reaction Monitoring (SRM) 676
Simon Hubbard 
676 
Selenoprotein 677
Enrique Blanco and Josep F. Abril 
677 
Self-Consistent Mean Field Algorithm 677
Roland Dunbrack 
677 
Self-Organizing Map (SOM, Kohonen Map) 678
John M. Hancock 
678 
Semantic Network 679
Robert Stevens 
679 
Semi-Global Alignment, see Global Alignment. 679
Seq-Gen 679
Michael P. Cummings 
679 
SeqCount, see ENCprime. 680
Sequence Alignment 680
Jaap Heringa 
680 
Sequence Assembly 680
Rodger Staden 
680 
Sequence Complexity (Sequence Simplicity) 680
Katheleen Gardiner 
680 
Sequence Conservation, see Conservation. 681
Sequence Distance Measures 681
Sudhir Kumar and Alan Filipski 
681 
Sequence Logo 682
Thomas D. Schneider 
682 
Sequence Motif, see Motif. 683
Sequence Motifs: Prediction and Modeling (Search by Signal) 683
Roderic Guigo 
683 
Sequence of a Protein 686
Roman Laskowski and Tjaart de Beer 
686 
Sequence Pattern 687
Roman Laskowski, Tjaart de Beer and Thomas D. Schneider 
687 
Sequence Read Archive (SRA, Short Read Archive) 687
Obi L. Griffith and Malachi Griffith 
687 
Sequence Retrieval System, see SRS. 688
Sequence Similarity 688
Jaap Heringa 
688 
Sequence Similarity-based Gene Prediction, see Gene Prediction, homology-based. 689
Sequence Similarity Search 689
Laszlo Patthy 
689 
Sequence Simplicity, see Sequence Complexity. 690
Sequence Tagged Site (STS) 690
John M. Hancock and Rodger Staden 
690 
Sequence Walker 690
Thomas D. Schneider 
690 
Serial Analysis of Gene Expression, see SAGE. 692
SGD (Saccharomyces Genome Database) 693
Obi L. Griffith and Malachi Griffith 
693 
Shannon Entropy (Shannon Uncertainty) 693
Thomas D. Schneider 
693 
Shannon Sphere 694
Thomas D. Schneider 
694 
Shannon Uncertainty, see Shannon Entropy. 695
Short-Period Interspersion, Short-Term Interspersion, see Interspersed Sequence. 695
Short Read Archive, see Sequence Read Archive. 695
Shuffle Test 695
David Jones 
695 
Side Chain 695
Roman Lask 
695 
Side-Chain Prediction 696
Roland Dunbrack 
696 
Signal-to-Noise Ratio, see Noise. 697
Signature, see Fingerprint. 697
SILAC, see Stable Isotope Labelling with Amino Acids in Cell Culture. 697
Silent Mutation, see Synonymous Mutation. 697
Similarity Index, see Distance Matrix. 697
SIMPLE (SIMPLE34) 697
John M. Hancock 
697 
Simple DNA Sequence (Simple Repeat, Simple Sequence Repeat) 698
John M. Hancock and Katheleen Gardiner 
698 
Simple Repeat, see Simple DNA Sequence. 698
Simple Sequence Repeat, see Simple DNA Sequence. 698
SIMPLE34, see SIMPLE. 698
Simulated Annealing 698
Roland Dunbrack 
698 
Simultaneous Alignment and Tree Building 699
Aidan Budd and Alexandros Stamatakis 
699 
Single Nucleotide Polymorphism (SNP) 699
Dov Greenbaum 
699 
Sippl Test, see Ungapped Threading Test B. 700
Sister Group 700
Aidan Budd and Alexandros Stamatakis 
700 
Site, see Character. 700
SITES 701
Michael P. Cummings 
701 
Small Sample Correction 701
Thomas D. Schneider 
701 
SMILES 702
Bissan Al-Lazikani 
702 
Smith-Waterman 702
Jaap Heringa 
702 
SNP, see Single Nucleotide Polymorphism. 702
Software Suites for Regulatory Sequences 703
Jacques van Helden 
703 
Solanaceae Genomics Network (SGN) 703
Dan Bolser 
703 
Solvation Free Energy 704
Roland Dunbrack 
704 
SOV 704
Patrick Aloy 
704 
Space-Filling Model 705
Eric Martz 
705 
SPARQL (SPARQL Protocol and RDF Query Language) 706
John M. Hancock 
706 
Spliced Alignment 706
Roderic Guigo 
706 
Splicing (RNA Splicing) 708
John M. Hancock 
708 
Split (Bipartition) 708
Aidan Budd and Alexandros Stamatakis 
708 
Spotted cDNA Microarray 708
Stuart Brown 
708 
SQL (Structured Query Language) 709
Matthew He 
709 
SRA, see Sequence Read Archive. 709
SRS (Sequence Retrieval System) 709
Guenter Stoesser 
709 
Stable Isotope Labelling with Amino Acids in Cell Culture (SILAC) 710
Simon Hubbard 
710 
STADEN 710
John M. Hancock and M.J. Bishop 
710 
Standard Genetic Code, see Genetic Code. 711
Standardized Qualitative Dynamical Systems 711
Luis Mendoza 
711 
Stanford HIV RT and Protease Sequence Database (HIV RT and Protease Sequence Database) 712
Guenter Stoesser, Malachi Griffith, Obi L. Griffith 
712 
Start Codon, see Genetic Code. 712
Statistical Mechanics 712
Patrick Aloy 
712 
Statistical Potential Energy 713
Roland Dunbrack 
713 
Steepest Descent Method, see Gradient Descent. 713
Stem-loop, see RNA hairpin. 713
Stochastic Process 714
Matthew He 
714 
Stop Codon, see Genetic Code. 714
Stream Mining (Time Series, Sequence, Data Stream, Data Flow) 714
Feng Chen and Yi-Ping Phoebe Chen 
714 
Strict Consensus Tree, see Consensus Tree. 715
Structural Alignment 715
Andrew Harrison and Christine Orengo 
715 
Structural Genomics 716
Jean-Michel Claverie 
716 
Structural Motif 717
Andrew Harrison and Christine Orengo 
717 
Structurama 718
Michael P. Cummings 
718 
Structure 718
Michael P. Cummings 
718 
Structure– 
719 
Andrew Harrison and Chris 
719 
Structure-Activity Relationship, see SAR. 720
Structure-based Drug Design (Rational Drug Design) 720
Marketa J. Zvelebil 
720 
STS, see Sequence Tagged Site. 720
Subfunctionalization 720
Austin L. Hughes 
720 
Substitution Process 721
Sudhir Kumar and Alan Filipski 
721 
Subtree 722
Aidan Budd and Alexandros Stamatakis 
722 
Superfamily 723
Dov Greenbaum 
723 
Superfold 723
Andrew Harrison and Christine Orengo 
723 
Supermatrix Approach 724
Aidan Budd and Alexandros Stamatakis 
724 
Supersecondary Structure 725
Roman Laskowski and Tjaart de Beer 
725 
Supertree, see Consensus Tree. 725
Supervised and Unsupervised Learning 725
Nello Cristianini 
725 
Support Vector Machine (SVM, Maximal Margin Classifier) 726
Nello Cristianini 
726 
Surface Models 727
Eric Martz 
727 
Surprisal 728
Thomas D. Schneider 
728 
SVM, see Support Vector Machine. 728
Swiss-Prot, see UniProt. 728
SwissModel 728
Roland Dunbrack 
728 
Symmetry Paradox 729
Thomas D. Schneider 
729 
Synapomorphy 730
A.R. Hoelzel 
730 
Synonymous Mutation (Silent Mutation) 731
Laszlo Patthy 
731 
Synteny 731
Dov Greenbaum 
731 
Systems Biology 732
Pascal Kahlem 
732 
T 733
Tandem Mass Spectrometry (MS) 735
Simon Hubbard 
735 
Tandem Repeat 735
Katheleen Gardiner 
735 
Tanimoto Distance 735
John M. Hancock 
735 
Target 736
Roland Dunbrack 
736 
TATA BOX 736
Niall Dillon 
736 
Taxonomic Classification (Organismal Classification) 736
Dov Greenbaum 
736 
Taxonomic Unit 738
Aidan Budd and Alexandros Stamatakis 
738 
Taxonomy 738
Robert Stevens 
738 
Telomere 738
Katheleen Gardiner 
738 
Template (Parent) 739
Roland Dunbrack 
739 
Template Gene Prediction, see Gene Prediction, ab initio. 739
Term 739
Robert Stevens 
739 
Terminology 739
Robert Stevens 
739 
Text Mining (Information Retrieval, IR) 739
Feng Chen and Yi-Ping Phoebe Chen 
739 
Thermal Noise 740
Thomas D. Schneider 
740 
Thesaurus 741
Robert Stevens 
741 
Thousand Genomes Project 741
Andrew Collins 
741 
THREADER, see Threading. 742
Threading 742
David Jones 
742 
TIM-barrel 742
Roman Laskowski and Tjaart de Beer 
742 
Trace Archive 743
Obi L. Griffith and Malachi Griffith 
743 
Tracer 743
Michael P. Cummings 
743 
Trans-Proteomic Pipeline (TPP) 744
Simon Hubbard 
744 
Transaction Database (Data Warehouse) 744
Feng Chen and Yi-Ping Phoebe Chen 
744 
Transcription 744
John M. Hancock 
744 
Transcription Factor 745
Jacques van Helden 
745 
Transcription Factor Binding Motif (TFBM) 745
Jacques van Helden 
745 
Transcription Factor Binding Site 746
Jacques van Helden 
746 
Transcription Factor Database 747
Jacques van Helden 
747 
Transcription Start Site (TSS) 748
John M. Hancock 
748 
Transcriptional Regulatory Region (Regulatory Sequence) 748
Niall Dillon and James Fickett 
748 
Transcriptome 748
Dov Greenbaum and Jean-Michel Claverie 
748 
TRANSFAC 749
Obi L. Griffith and Malachi Griffith 
749 
Transfer RNA (tRNA) 750
Robin R. Gutell 
750 
Translation 752
John M. Hancock 
752 
Translation End Site 752
Enrique Blanco and Josep F. Abril 
752 
Translation Start Site 753
Roderic Guigo 
753 
Translatome 754
Dov Greenbaum 
754 
Transposable Element (Transposon) 754
Dov Greenbaum and Katheleen Gardiner 
754 
Transposon, see Transposable Element. 755
Tree, see Phylogenetic Tree. 756
Tree of Life 756
Sudhir Kumar and Alan Filipski 
756 
Tree-based Progressive Alignment 756
Jaap Heringa 
756 
Tree-Puzzle, see Quartets, Phylogenetic. 757
TreeStat 757
Michael P. Cummings 
757 
Tree Topology 758
Aidan Budd and Alexandros Stamatakis 
758 
Tree Traversal 759
Aidan Budd and Alexandros Stamatakis 
759 
TreeView X 759
Michael P. Cummings 
759 
Trinucleotide Repeat 760
Katheleen Gardiner 
760 
Triple Store, see Database. 760
tRNA, see Transfer RNA. 760
Turn 760
Roman Laskowski and Tjaart de Beer 
760 
Twilight Zone 761
Teresa K. Attwood 
761 
Two-Dimensional Gel Electrophoresis (2DE) 762
Dov Greenbaum 
762 
Type Genome see Reference Genome 763
U 765
UCSC Genome Browser 767
Obi L. Griffith and Malachi Griffith 
767 
Uncertainty 768
Thomas D. Schneider 
768 
Ungapped Threading Test B (Sippl Test) 768
David Jones 
768 
Unigene 769
Malachi Griffith and Obi L. Griffith 
769 
UniProt 769
Marketa J. Zvelebil 
769 
Universal Genetic Code, see Genetic Code. 770
Unsupervised Learning, see Supervised and Unsupervised Learning. 770
Unrooted Phylogenetic Tree, see Phylogenetic Tree. 770
Unscaled Phylogenetic Tree, see Branch. 770
UPGMA 770
Sudhir Kumar and Alan Filipski 
770 
Upstream 771
Niall Dillon 
771 
V 773
Validation Measures for Clustering 775
Pedro Larran˜ aga and Concha Bielza 
775 
Variance Components (Components of Variance, VC) 775
Mark McCarthy and Steven Wiltshire 
775 
Variation (Genetic) 777
Matthew He 
777 
VarioML 777
John M. Hancock 
777 
VAST (Vector Alignment Search Tool) 778
John M. Hancock and M.J. Bishop 
778 
VC, see Variance Components. 778
Vector, see Data Structure. 779
Vector Alignment Search Tool, see VAST. 779
VecScreen 779
John M. Hancock and M.J. Bishop 
779 
VectorNTI 779
John M. Hancock 
779 
VEGA (Vertebrate Genome Annotation Database) 779
Obi L. Griffith and Malachi Griffith 
779 
Vertebrate Genome Annotation Database, see VEGA. 780
Virtual Library 780
Bissan Al-Lazikani 
780 
Virtual Screening 781
Bissan Al-Lazikani 
781 
Virtualization 781
James Marsh, David Thorne and Steve Pettifer 
781 
VISTA 782
John M. Hancock 
782 
Visualization, Molecular 782
Eric Martz 
782 
Visualization of Multiple Sequence Alignments – Physicochemical Properties 784
Teresa K. Attwood 
784 
W 787
Web Ontology Language (OWL) 789
John M. Hancock 
789 
Web Services 789
Carole Goble and Katy Wolstencroft 
789 
Weight Matrix, see Sequence Motifs: Prediction and Modeling. 789
Whatcheck 790
Roland Dunbrack 
790 
WhatIf 790
Roland Dunbrack 
790 
WormBase 790
Obi L. Griffith and Malachi Griffith 
790 
WSDL/SOAP Web Services 791
Carole Goble and Katy Wolstencroft 
791 
X 793
X-Ray Crystallography for Structure Determination 795
Liz Carpenter 
795 
X Chromosome, see Sex Chromosome. 795
Xenbase 796
Dan Bolser 
796 
Xenolog (Xenologue) 796
Laszlo Patthy 
796 
XML (eXtensible Markup Language) 796
Eric Martz 
796 
Y 799
Yeast Deletion Project (YDPM) 801
Dan Bolser 
801 
Yule Process 801
Matthew He 
801 
Z 803
z-score 805
Matthew He 
805 
Zero Base, see Zero Coordinate. 805
Zero Coordinate (Zero Base, Zero Position) 805
Thomas D. Schneider 
805 
Zero Position, see Zero Coordinate. 805
Zeta Virtual Dihedral Angle 805
Roman Laskowski and Tjaart de Beer 
805 
Zipf' 
805 
Author Index 807
Supplementary images 825

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: 18.11.2013
• 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: 1-118-59816-4 / 1118598164
• ISBN-13: 978-1-118-59816-0 / 9781118598160