Combinatorics of genome rearrangements:
Gespeichert in:
| Format: | Buch |
|---|---|
| Sprache: | English |
| Veröffentlicht: |
Cambridge, Mass. [u.a.]
MIT Press
2009
|
| Schriftenreihe: | Computational molecular biology
|
| Schlagworte: | |
| Online-Zugang: | Inhaltstext Inhaltsverzeichnis |
| Beschreibung: | Includes bibliographical references (p. [263]-282) and index |
| Beschreibung: | XI, 288 S. graph. Darst. 24 cm |
| ISBN: | 9780262062824 0262062828 |
Internformat
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| 650 | 4 | |a Combinatorial analysis | |
| 650 | 4 | |a Gene Rearrangement | |
| 650 | 4 | |a Genome | |
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Datensatz im Suchindex
| _version_ | 1804140939136991232 |
|---|---|
| adam_text | COMBINATORICS OF GENOME REARRANGEMENTS GUILLAUME FERTIN, ANTHONY
LABARRE, IRENA RUSU, ERIC TANNIER AND STEPHANE VIALETTE THE MIT PRESS
CAMBRIDGE, MASSACHUSETTS LONDON, ENGLAND CONTENTS PREFACE XIII
ACKNOWLEDGMENTS XV INTRODUCTION 1 1.1 A MINIMALIST INTRODUCTION TO
MOLECULAR EVOLUTION 1 1.2 BIRTH OF THE COMBINATORICS OF GENOME
REARRANGEMENTS ^ 1.3 STATEMENT OF THE PROBLEM 6 1.4 SCOPE OF THIS SURVEY
7 1.5 OVERVIEW OF THE MODELS 7 1.6 ORGANIZATION OF THE BOOK 8
DUPLICATION-FREE MODELS: PERMUTATIONS 11 GENOMES AS PERMUTATIONS 13 2.1
THE SYMMETRIC GROUP 13 2.2 THE CYCLES OF A PERMUTATION 14 2.3 SIGNED
PERMUTATIONS 15 2.4 DISTANCES ON PERMUTATION GROUPS 15 2.4.1
REARRANGEMENTS AS GENERATORS 16 2.4.2 INVARIANT DISTANCES 17 2.5
CIRCULAR PERMUTATIONS 18 2.5.1 CLASSICAL CIRCULAR PERMUTATIONS 19 2.5.2
GENOMIC CIRCULAR PERMUTATIONS 19 2.6 FIRST MEASURES OF SIMILARITY
BETWEEN PERMUTATIONS 20 2.6.1 BREAKPOINTS 20 2.6.2 COMMON INTERVALS AND
SEMIPARTITIVE FAMILIES 21 DISTANCES BETWEEN UNSIGNED PERMUTATIONS 25 3.1
TRANSPOSITION DISTANCE 25 3.1.1 LOWER BOUNDS ON THE TRANSPOSITION
DISTANCE 26 3.1.2 UPPER BOUNDS 29 3.1.3 IMPROVING BOUNDS USING TORIC
PERMUTATIONS 32 CONTENTS 3.2 3.3 3.4 3.5 3.1.4 3.1.5 3.1.6 PREFIX 3.2.1
3.2.2 3.2.3 3.2.4 3.2.5 3.2.6 EASY CASES 33 APPROXIMATION ALGORITHMS 34
CONJECTURES AND OPEN PROBLEMS 35 TRANSPOSITION DISTANCE 36 LOWER BOUNDS
37 UPPER BOUNDS 38 DIAMETER 38 EASY CASES 39 APPROXIMATION ALGORITHMS 39
VARIANT: INSERTION OF THE LEADING ELEMENT 40 REVERSAL DISTANCE 40 3.3.1
3.3.2 3.3.3 3.3.4 3.3.5 3.3.6 PREFIX 3.4.1 3.4.2 3.4.3 LOWER BOUNDS 40
UPPER BOUNDS 43 EASY CASES 43 COMPUTATIONAL COMPLEXITY 44 APPROXIMATION
ALGORITHMS 45 EXACT ALGORITHMS 46 REVERSAL DISTANCE (PANCAKE-FLIPPING)
47 LOWER BOUNDS 47 HISTORY 48 VARIANTS 48 VARIANTS 49 3.5.1 3.5.2 3.5.3
3.5.4 3.5.5 3.5.6 3.5.7 3.5.8 3.5.9 3.5.10 BLOCK INTERCHANGE DISTANCE 49
ELEMENT INTERCHANGE DISTANCES 50 WEIGHTED REVERSALS 52 FIXED-LENGTH
REVERSALS 54 BOUNDED VARIANTS 54 CUT-AND-PASTE 55 STRIP MOVES 55
STACK-SORTING 56 TANDEM DUPLICATIONS AND RANDOM LOSSES 58 COMBINED
OPERATIONS: REVERSALS AND TRANSPOSITIONS 59 3.6 RELATIONS BETWEEN
DISTANCES ON UNSIGNED PERMUTATIONS 61 DISTANCES BETWEEN SIGNED
PERMUTATIONS 63 4.1 CONSERVED INTERVAL DISTANCE 63 4.2 SIGNED REVERSAL
DISTANCE 64 4.2.1 REVERSALS 64 4.2.2 THE DISTANCE FORMULA 65 4.2.3 THE
SCENARIO OF REVERSALS 67 4.2.4 THE SPACE OF ALL OPTIMAL SOLUTIONS 68
4.2.5 EXPERIMENTAL RESULTS 69 4.3 VARIANTS OF SORTING BY REVERSALS 69
4.3.1 PERFECT SIGNED REVERSAL DISTANCE 69 4.3.2 PREFIX REVERSALS (BURNED
PANCAKES) 70 4.3.3 REVERSALS THAT ARE SYMMETRIC AROUND A POINT 70
CONTENTS VII 4.3.4 WEIGHTED REVERSALS 71 4.3.5 FIXED-LENGTH REVERSALS 71
4.4 COMBINED OPERATIONS 72 4.4.1 REVERSALS AND TRANSPOSITIONS 72 4.4.2
REVERSALS, TRANSPOSITIONS, TRANSREVERSALS, REVREVS 72 4.5 DOUBLE
CUT-AND-JOINS 73 5 REARRANGEMENTS OF PARTIAL ORDERS 75 5.1 GENOMES AS
PARTIALLY ORDERED SETS 75 5.2 PARTIALLY ORDERED SETS 75 5.2.1 BASIC
DEFINITIONS 75 5.2.2 REPRESENTING POSETS 77 5.2.3 TOPOLOGICAL SORTING 77
5.3 CONSTRUCTING A POSET 78 5.4 REVERSAL DISTANCE 79 5.5 BREAKPOINT
DISTANCE 80 5.5.1 EXACT ALGORITHMS 80 5.5.2 HEURISTICS FOR COMPUTING THE
BREAKPOINT DISTANCE 81 6 GRAPH-THEORETIC AND LINEAR ALGEBRA FORMULATIONS
83 6.1 SIMPLE PERMUTATIONS AND THE INTERLEAVING GRAPH 83 6.2 THE OVERLAP
GRAPH 84 6.3 THE LOCAL COMPLEMENTATION OF A GRAPH 85 6.4 THE MATRIX
TIGHTNESS PROBLEM 85 6.5 EXTENSION TO SORTING BY TRANSPOSITIONS 86 6.6
THE INTERMEDIATE CASE OF DIRECTED LOCAL COMPLEMENTATION 87 II MODELS
HANDLING DUPLICATIONS: STRINGS 89 7 GENERALITIES 91 7.1 BIOLOGICAL
MOTIVATIONS 91 7.2 STRINGS AND REARRANGEMENTS ON STRINGS 92 7.3 BALANCED
STRINGS 94 7.4 HOW TO DEAL WITH MULTIPLE COPIES? 95 8 DISTANCES BETWEEN
ARBITRARY STRINGS 97 8.1 THE MATCH-AND-PRUNE MODEL 98 8.1.1 BREAKPOINT
DISTANCE 100 8.1.2 SIGNED REVERSAL DISTANCE 106 8.1.3 ADJACENCY
SIMILARITY 108 8.1.4 COMMON INTERVALS SIMILARITY 111 8.1.5 CONSERVED
INTERVALS SIMILARITY 113 8.1.6 CONSERVED INTERVALS DISTANCE 114 8.1.7
MAD AND SAD NUMBERS 118 8.1.8 HEURISTICS 119 VIII CONTENTS 8.2 THE BLOCK
EDIT MODEL 123 8.2.1 BLOCK COVERING DISTANCE 123 8.2.2 SYMMETRIC BLOCK
EDIT DISTANCE 126 8.2.3 LARGE BLOCK EDIT DISTANCE 129 8.2.4 STRING EDIT
DISTANCE WITH TRANSPOSITIONS 130 8.2.5 SIGNED STRINGS 131 9 DISTANCES
BETWEEN BALANCED STRINGS 133 9.1 MINIMUM COMMON STRING PARTITION
PROBLEMS 133 9.1.1 UNSIGNED MCSP 134 9.1.2 SIGNED MCSP 135 9.1.3
REVERSED MCSP 137 9.1.4 FULL BREAKPOINT DISTANCE 138 9.2 REVERSAL
DISTANCE 138 9.2.1 UNSIGNED REVERSALS 138 9.2.2 SIGNED REVERSALS 141
9.2.3 SORTING BY REVERSALS WITH LENGTH-WEIGHTED COSTS 142 9.2.4 PREFIX
REVERSALS ON UNSIGNED STRINGS (PANCAKE-FLIPPING) 144 9.2.5 REVERSALS OF
LENGTH AT MOST 2 147 9.3 UNSIGNED TRANSPOSITIONS 147 9.3.1 UNIT COST
TRANSPOSITIONS 147 9.3.2 LENGTH-WEIGHTED TRANSPOSITIONS 150 9.3.3
RESTRICTED LENGTH-WEIGHTED TRANSPOSITIONS 150 9.3.4 PREFIX
TRANSPOSITIONS 152 9.3.5 ADJACENT SWAPS 153 9.4 UNSIGNED BLOCK
INTERCHANGES 153 9.4.1 UNIT-COST BLOCK INTERCHANGES 153 9.4.2 CHARACTER
SWAPS 155 9.5 RELATIONS BETWEEN DISTANCES 157 III MULTICHROMOSOMAL
MODELS 159 10 PATHS AND CYCLES 161 10.1 GENOMES 161 10.2 BREAKPOINTS 162
10.3 INTERVALS 163 10.4 TRANSLOCATION DISTANCE 164 10.4.1 FEASIBILITY
166 10.4.2 UNSIGNED GENOMES 166 10.4.3 SIGNED GENOMES 167 10.4.4
TRANSLOCATIONS PRESERVING CENTROMERES 168 10.4.5 VARIANTS AND SPECIAL
CASES 169 10.5 DOUBLE CUT-AND-JOINS (2-BREAK REARRANGEMENT) 170 10.6
/(-BREAK REARRANGEMENT 171 10.7 FUSIONS, FISSIONS, TRANSLOCATIONS, AND
REVERSALS 172 10.8 REARRANGEMENTS WITH PARTIALLY ORDERED CHROMOSOMES 174
CONTENTS IX 11 CYCLES OF A PERMUTATION 175 11.1 A MODEL FOR
MULTICHROMOSOMAL CIRCULAR GENOMES 175 11.2 A GENERALIZATION TO SIGNED
GENOMES 178 11.2.1 A DIFFERENT KIND OF SIGNED PERMUTATION 178 11.2.2 THE
OPERATIONS 179 11.2.3 SOME RESULTS 179 12 SET SYSTEMS AND THE SYNTENIC
DISTANCE 181 12.1 INTRODUCTION 181 12.2 STRUCTURAL PROPERTIES 182 12.2.1
COMPACT REPRESENTATION 182 12.3 LOWER BOUNDS 184 12.4 DIAMETER 185 12.5
ALGORITHMIC RESULTS 185 12.5.1 SYNTENIC DISTANCE 185 12.5.2 EASY CASES
186 12.6 CONJECTURES AND OPEN PROBLEMS 189 IV MULTIGENOMIC MODELS 191 13
MEDIAN AND HALVING PROBLEMS 193 13.1 BREAKPOINT MEDIAN 194 13.1.1
COMPLEXITY 194 13.1.2 ALGORITHMS 195 13.2 REVERSAL AND DCJ MEDIAN 197
13.2.1 COMPLEXITY 197 13.2.2 ALGORITHMS 197 13.2.3 VARIANTS 198 13.3
DUPLICATED GENOMES 199 13.3.1 THE DOUBLE DISTANCE 199 13.3.2 GENOME
HALVING 201 13.3.3 SOLVING TETRAPLOIDY 202 13.3.4 GUIDED HALVING 202
13.3.5 GENOME HALVING WITH UNORDERED CHROMOSOMES 203 13.4 OTHER
VARIANTS, GENERALIZATIONS, AND DISCUSSION 205 13.4.1 OTHER OPERATIONS
205 13.4.2 MORE PERMUTATIONS IN THE INPUT 205 13.4.3 MEDIANS AND CENTERS
205 13.4.4 DISCUSSION 206 14 REARRANGEMENT PHYLOGENIES 207 14.1 THE
LARGE PARSIMONY PROBLEM 207 14.2 THE LARGE PARSIMONY PROBLEM WITH GENE
ORDERS 209 14.2.1 BREAKPOINT AND REVERSAL PHYLOGENIES ON PERMUTATIONS
209 14.2.2 VARIANTS 211 CONTENTS 14.3 HEURISTICS FOR THE
BREAKPOINT/REVERSAL PHYLOGENY PROBLEM 211 14.3.1 TREE STEINERIZATION 212
14.3.2 SEQUENTIAL ADDITION 216 14.3.3 CHARACTER ENCODINGS 217 14.4
VARIANTS 220 V MISCELLANEOUS 221 15 SOFTWARE 223 15.1 PAIRWISE
REARRANGEMENTS 223 15.1.1 UNICHROMOSOMAL MODELS 223 15.1.2
MULTICHROMOSOMAL MODELS 225 15.2 PHYLOGENY RECONSTRUCTION AND MEDIANS
226 15.2.1 BPANALYSIS 226 15.2.2 MGR 226 15.2.3 GRIL 226 15.2.4 GRAPPA
227 15.2.5 MEDRBYLS 227 15.2.6 REVOLUZER AND AMGRP 227 15.2.7 GENESIS
228 16 OPEN PROBLEMS 229 16.1 COMPLEXITY ISSUES 229 16.1.1 HARDNESS 229
16.1.2 APPROXIMABILITY 230 16.1.3 POLYNOMIAL COMPLEXITY 231 16.2
DIAMETER 231 16.3 TIGHTNESS OF BOUNDS 232 APPENDICES 233 A GRAPH THEORY
235 A.1 UNDIRECTED GRAPHS 235 A.1.1 BASIC DEFINITIONS 235 A.1.2 PATHS
AND CYCLES 236 A.1.3 CONNECTIVITY 237 A. 1.4 BIPARTITE GRAPHS 238 A.1.5
TREES AND FORESTS 238 A. 1.6 MATCHING 238 A.1.7 ADJACENCY MATRIX 239 A.2
DIRECTED GRAPHS 240 A.2.1 BASIC DEFINITIONS 240 A.2.2 PATHS AND CYCLES
241 A.2.3 CONNECTIVITY 241 A.2.4 DIRECTED ACYCLIC GRAPHS 241 CONTENTS
COMPLEXITY THEORY 243 B.1 THE CLASS NP 243 B.1.1 NP-OPTIMIZATION
PROBLEMS: FROM PTAS TO APX 246 B.1.2 NP-OPTIMIZATION PROBLEMS: BEYOND
APX 25 0 B.1.3 PARAMETERIZED COMPLEXITY 250 B.2 SOME NP-COMPLETE
PROBLEMS 252 GLOSSARY 257 BIBLIOGRAPHY 263 INDEX 283
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| id | DE-604.BV035948014 |
| illustrated | Illustrated |
| indexdate | 2024-07-09T22:07:56Z |
| institution | BVB |
| isbn | 9780262062824 0262062828 |
| language | English |
| lccn | 2008042152 |
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| owner | DE-91G DE-BY-TUM DE-83 DE-19 DE-BY-UBM |
| owner_facet | DE-91G DE-BY-TUM DE-83 DE-19 DE-BY-UBM |
| physical | XI, 288 S. graph. Darst. 24 cm |
| publishDate | 2009 |
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| publishDateSort | 2009 |
| publisher | MIT Press |
| record_format | marc |
| series2 | Computational molecular biology |
| spelling | Combinatorics of genome rearrangements Guillaume Fertin ... Cambridge, Mass. [u.a.] MIT Press 2009 XI, 288 S. graph. Darst. 24 cm txt rdacontent n rdamedia nc rdacarrier Computational molecular biology Includes bibliographical references (p. [263]-282) and index Translocation (Genetics) / Mathematical models Translocation (Genetics) / Data processing Combinatorial analysis Genomics / Mathematics Analyse combinatoire Rameau Génome - Mathématiques Rameau Réarrangement génétique Rameau Translocation (génétique) - Modèles mathématiques Rameau Datenverarbeitung Mathematik Mathematisches Modell Gene Rearrangement Genome Genomics Mathematics Models, Genetic Translocation (Genetics) Data processing Translocation (Genetics) Mathematical models Kombinatorik (DE-588)4031824-2 gnd rswk-swf Genom (DE-588)4156640-3 gnd rswk-swf Genom (DE-588)4156640-3 s Kombinatorik (DE-588)4031824-2 s DE-604 Fertin, Guillaume 1972- Sonstige (DE-588)138898146 oth DE-601 pdf/application http://www.zentralblatt-math.org/zmath/en/search/?an=1170.92022 Zentralblatt MATH kostenfrei Inhaltstext HEBIS Datenaustausch application/pdf http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=018805127&sequence=000001&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA Inhaltsverzeichnis |
| spellingShingle | Combinatorics of genome rearrangements Translocation (Genetics) / Mathematical models Translocation (Genetics) / Data processing Combinatorial analysis Genomics / Mathematics Analyse combinatoire Rameau Génome - Mathématiques Rameau Réarrangement génétique Rameau Translocation (génétique) - Modèles mathématiques Rameau Datenverarbeitung Mathematik Mathematisches Modell Gene Rearrangement Genome Genomics Mathematics Models, Genetic Translocation (Genetics) Data processing Translocation (Genetics) Mathematical models Kombinatorik (DE-588)4031824-2 gnd Genom (DE-588)4156640-3 gnd |
| subject_GND | (DE-588)4031824-2 (DE-588)4156640-3 |
| title | Combinatorics of genome rearrangements |
| title_auth | Combinatorics of genome rearrangements |
| title_exact_search | Combinatorics of genome rearrangements |
| title_full | Combinatorics of genome rearrangements Guillaume Fertin ... |
| title_fullStr | Combinatorics of genome rearrangements Guillaume Fertin ... |
| title_full_unstemmed | Combinatorics of genome rearrangements Guillaume Fertin ... |
| title_short | Combinatorics of genome rearrangements |
| title_sort | combinatorics of genome rearrangements |
| topic | Translocation (Genetics) / Mathematical models Translocation (Genetics) / Data processing Combinatorial analysis Genomics / Mathematics Analyse combinatoire Rameau Génome - Mathématiques Rameau Réarrangement génétique Rameau Translocation (génétique) - Modèles mathématiques Rameau Datenverarbeitung Mathematik Mathematisches Modell Gene Rearrangement Genome Genomics Mathematics Models, Genetic Translocation (Genetics) Data processing Translocation (Genetics) Mathematical models Kombinatorik (DE-588)4031824-2 gnd Genom (DE-588)4156640-3 gnd |
| topic_facet | Translocation (Genetics) / Mathematical models Translocation (Genetics) / Data processing Combinatorial analysis Genomics / Mathematics Analyse combinatoire Génome - Mathématiques Réarrangement génétique Translocation (génétique) - Modèles mathématiques Datenverarbeitung Mathematik Mathematisches Modell Gene Rearrangement Genome Genomics Mathematics Models, Genetic Translocation (Genetics) Data processing Translocation (Genetics) Mathematical models Kombinatorik Genom |
| url | http://www.zentralblatt-math.org/zmath/en/search/?an=1170.92022 http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=018805127&sequence=000001&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA |
| work_keys_str_mv | AT fertinguillaume combinatoricsofgenomerearrangements |