Concise Encyclopaedia of Bioinformatics and Computational Biology -- Title Page -- Copyright -- Contents -- List of Contributors -- Preface -- A -- Ab Initio -- Ab Initio Gene Prediction, see Gene Prediction, ab initio. -- ABNR, see Energy Minimization. -- Accuracy (of Protein Structure Prediction) -- David Jones -- Accuracy Measures, see Error Measures. -- Adjacent Group -- Aidan Budd and Alexandros Stamatakis -- Admixture Mapping (Mapping by Admixture Linkage Disequilibrium) -- Andrew Collins, Mark McCarthy and Steven Wiltshire -- Adopted-basis Newton- Raphson Minimization (ABNR), see Energy Minimization. -- Affine Gap Penalty, see Gap Penalty. -- Affinity Propagation-based Clustering -- Pedro Larran aga and Concha Bielza -- Affymetrix GeneChip™ Oligonucleotide Microarray -- Stuart Brown and Dov Greenbaum -- Affymetrix Probe Level Analysis -- Stuart Brown -- After Sphere, see After State. -- After State (After Sphere) -- Thomas D. Schneider -- AIC, see Akaike Information Criterion. -- Akaike Information Criterion -- Pedro Larranaga and Concha Bielza -- Algorithm -- Matthew He -- Alignment (Domain Alignment, Repeats Alignment) -- Jaap Heringa -- Alignment Score -- Laszlo Patthy -- Allele-Sharing Methods (Non-parametric Linkage Analysis) -- Mark McCarthy, Steven Wiltshire and Andrew Collins -- Allelic Association -- Mark McCarthy, Steven Wiltshire and Andrew Collins -- Allen Brain Atlas -- Dan Bolser -- Allopatric Evolution (Allopatric Speciation) -- A.R. Hoelzel -- Allopatric Speciation, see Allopatric Evolution. -- AlogP -- Bissan Al-Lazikani -- Alpha carbon, see Cα (C-Alpha). -- Alpha Helix -- Roman Laskowski and Tjaart de Beer -- Alternative Splicing -- Enrique Blanco and Josep F. Abril.

Alternative Splicing Gene Prediction, see Gene Prediction, alternative splicing. -- Amide Bond (Peptide Bond) -- Roman Laskowski and Tjaart de Beer -- Amino Acid (Residue) -- Roman Laskowski, Jeremy Baum and Tjaart de Beer -- Amino Acid Abbreviations, see IUPAC-IUB Codes. -- Amino Acid Composition -- Jeremy Baum -- Amino Acid Exchange Matrix (Dayhoff Matrix, Log Odds Score, PAM (Matrix), BLOSUM Matrix) -- Jaap Heringa -- AMINO Acid Substitution Matrix, see Amino Acid Exchange Matrix. -- Amino-terminus, see N-terminus. -- Amphipathic -- Roman Laskowski and Tjaart de Beer -- Analog (Analogue) -- Dov Greenbaum -- Ancestral Lineage, see Offspring Lineage. -- Ancestral State Reconstruction -- Sudhir Kumar and Alan Filipski -- Anchor Points -- Roland Dunbrack -- Annotation Refinement Pipelines, see Gene Prediction. -- Annotation Transfer (Guilt by Association Annotation) -- Dov Greenbaum -- APBIONET (Asia-Pacific Bioinformatics Network) -- Pedro Fernandes -- Apomorphy -- A.R. Hoelzel -- APOLLO, see Gene Annotation, visualization tools. -- Arc, see Branch (of a Phylogenetic Tree). -- Are We There Yet?, see AWTY. -- Aromatic -- Roman Laskowski and Tjaart de Beer -- Array, see Data Structure. -- Artificial Neural Networks, see Neural Networks. -- ASBCB (The African Society for Bioinformatics and Computational Biology) -- Pedro Fernandes -- Association Analysis (Linkage Disequilibrium Analysis) -- Andrew Collins, Mark McCarthy and Steven Wiltshire -- Association Rule, see Association Rule Mining. -- Association Rule Mining (Frequent Itemset, Association Rule, Support, Confidence, Correlation Analysis) -- Feng Chen and Yi-Ping Phoebe Chen -- Associative Array, see Data Structure. -- Asymmetric Unit -- Liz Carpenter -- Atomic Coordinate File (PDB file) -- Eric Martz -- Autapomorphy -- A.R. Hoelzel.

Autozygosity, see Homozygosity, Homozygosity Mapping. -- AWTY (Are We There Yet?) -- Michael P. Cummings -- Axiom -- Robert Stevens -- B -- Backbone (Main Chain) -- Roman Laskowski and Tjaart de Beer -- Backbone Models -- Eric Martz -- Backpropagation Networks, see Neural Networks. -- Bagging -- Concha Bielza and Pedro Larranaga -- Ball and Stick Models -- Eric Martz -- BAMBE (Bayesian Analysis in Molecular Biology and Evolution) -- Michael P. Cummings -- Base-Call Confidence Values -- Rodger Staden and John M. Hancock -- Base Composition (GC Richness, GC Composition) -- Katheleen Gardiner -- Bayes' Theorem -- Feng Chen, Yi-Ping Phoebe Chen and Matthew He -- Bayesian Classifier (Naive Bayes) -- Pedro Larranaga and Concha Bielza -- Bayesian Evolutionary Analysis Utility, see BEAUti. -- Bayesian Information Criterion (BIC) -- Concha Bielza and Pedro Larranaga -- Bayesian Network (Belief Network, Probabilistic Network, Causal Network, Knowledge Map) -- John M Hancock -- Bayesian Phylogenetic Analysis -- Sudhir Kumar and Alan Filipski -- BEAGLE -- Michael P. Cummings -- Beam Search -- Concha Bielza and Pedro Larranaga -- BEAST (Bayesian Evolutionary Analysis by Sampling Trees) -- Michael P. Cummings -- BEAUti (Bayesian Evolutionary Analysis Utility) -- Michael P. Cummings -- Before State (Before Sphere) -- Thomas D. Schneider -- Belief Network, see Bayesian Network. -- Bemis and Murcko Framework (Murcko Framework) -- Bissan Al-Lazikani -- Best-First Search -- Concha Bielza and Pedro Larranaga -- Beta Barrel -- Roman Laskowski -- Beta Breaker -- Patrick Aloy -- Beta Sheet -- Roman Laskowski and Tjaart de Beer -- Beta Strand -- Roman Laskowski and Tjaart de Beer -- BIC, see Bayesian Information Criterion. -- Biclustering Methods -- Pedro Larran aga and Concha Bielza -- Bifurcation (in a Phylogenetic Tree).

Aidan Budd and Alexandros Stamatakis -- Binary Numerals -- John M. Hancock -- Binary Relation -- Robert Stevens -- Binary Tree, see Data Structure. -- Binding Affinity (Kd, Ki, IC50) -- Bissan Al-Lazikani and John M. Hancock -- Binding Site -- Thomas D. Schneider -- Binding Site Symmetry -- Thomas D. Schneider -- Bio++ -- Michael P. Cummings -- Bioactivity Database -- Bissan Al-Lazikani -- Bioinformatics (Computational Biology) -- John M. Hancock -- The Bioinformatics Organization, Inc (formerly bioinformatics.org) -- Pedro Fernandes -- Bioinformatics Training Network, see BTN. -- Biological Identifiers -- Carole Goble and Katy Wolstencroft -- BioMart -- Obi L. Griffith and Malachi Griffith -- Bipartition, see Split -- Bit -- Thomas D. Schneider -- BLAST (Maximal Segment Pair, MSP) -- Jaap Heringa -- BLASTX -- Roderic Guigo -- BLAT (BLAST-like Alignment Tool) -- J.M. Hancock -- BLOSUM (BLOSUM Matrix) -- Laszlo Patthy -- Boltzmann Factor -- Roman Laskowski and Tjaart de Beer -- Boolean Logic -- James Marsh, David Thorne and Steve Pettifer -- Boosting -- Concha Bielza and Pedro LarranËœ aga -- Bootstrap Analysis, see Bootstrapping. -- Bootstrapping (Bootstrap Analysis) -- Aidan Budd and Alexandros Stamatakis -- Bottleneck, see Population Bottleneck. -- Box -- Thomas D. Schneider -- Branch (of a Phylogenetic Tree) (Edge, Arc) -- Aidan Budd and Alexandros Stamatakis -- Branch Length, see Branch, Branch-length Estimation. -- Branch-length Estimation -- Sudhir Kumar and Alan Filipski -- BTN (Bioinformatics Training Network) -- Pedro Fernandes -- C -- C-α (C-alpha) -- Cancer Gene Census (CGC) -- Malachi Griffith and Obi L. Griffith -- Candidate Gene (Candidate Gene-based Analysis) -- Mark McCarthy, Steven Wiltshire and Andrew Collins -- Carboxy-Terminus, see C-Terminus. -- CASP -- David Jones.

Catalogue of Somatic Mutations in Cancer, see COSMIC -- Catalytic Triad -- Roman Laskowski and Tjaart de Beer -- Category -- Robert Stevens -- Causal Network, see Bayesian Network -- CCDS (Consensus Coding Sequence Database) -- Obi L. Griffith and Malachi Griffith -- CDS, see Coding Region. -- Centimorgan -- Katheleen Gardiner -- Centromere (Primary Constriction) -- Katheleen Gardiner -- CGC, see Cancer Gene Census. -- Channel Capacity (Channel Capacity Theorem) -- Thomas D. Schneider -- Character (Site) -- Sudhir Kumar and Alan Filipski -- CHARMM -- Roland Dunbrack -- Chemical Biology -- Bissan Al-Lazikani -- Chemical Hashed Fingerprint -- Bissan Al-Lazikani -- Chemoinformatics -- Bissan Al-Lazikani -- ChIP-seq -- Stuart Brown -- Chou & Fasman Prediction Method -- Patrick Aloy -- Chromatin -- Katheleen Gardiner -- Chromosomal Deletion -- Katheleen Gardiner -- Chromosomal Inversion -- Katheleen Gardiner -- Chromosomal Translocation -- Katheleen Gardiner -- Chromosome -- Katheleen Gardiner -- Chromosome Band -- Katheleen Gardiner -- Circos, see Gene Annotation, visualization tools. -- Cis-regulatory Element -- Jacques van Helden -- Cis-regulatory Module (CRM) -- Jacques van Helden -- Cis-regulatory Module Prediction -- Jacques van Helden -- Clade (Monophyletic Group) -- Aidan Budd and Alexandros Stamatakis -- Cladistics -- Aidan Budd and Alexandros Stamatakis -- Clan -- Aidan Budd and Alexandros Stamatakis -- Classification -- Robert Stevens -- Classification in Machine Learning (Discriminant Analysis) -- Nello Cristianini -- Classifier (Reasoner) -- Robert Stevens -- Classifiers, Comparison -- Pedro Larran aga and Concha Bielza -- Clogp -- Bissan Al-Lazikani -- CLUSTAL -- Jaap Heringa -- Clustal Omega, see Clustal. -- ClustalW, see Clustal -- ClustalX, see Clustal. -- Cluster -- Dov Greenbaum.

Cluster Analysis, see Clustering.