Verfügbarkeit: Bioinformatics algorithms

Bioinformatics algorithms: sequence analysis, genome rearrangements, and phylogenetic reconstruction

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Bibliographische Detailangaben
1. Verfasser:	Ohlebusch, Enno (VerfasserIn)
Format:	Buch
Sprache:	English
Veröffentlicht:	Ulm <<E.>> Ohlebusch 2013
Online-Zugang:	Inhaltsverzeichnis
Beschreibung:	Literaturangaben
Beschreibung:	XVI, 604 S. graph. Darst. 24 cm
ISBN:	9783000413162

Internformat

MARC


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Datensatz im Suchindex

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adam_text	CONTENTS PREFACE XIII 1 MOLECULAR BIOLOGY IN A NUTSHELL 1 1.1 NUCLEIC ACIDS AND PROTEINS 1 1.2 EVOLUTION 7 2 EXACT STRING MATCHING 9 2.1 BASIC STRING DEFINITIONS 9 2.2 THE NAIVE ALGORITHM 11 2.3 THE BOYER-MOORE-HORSPOOL ALGORITHM 12 2.4 THE KNUTH-MORRIS-PRATT ALGORITHM 15 2.5 THE AHO-CORASICK ALGORITHM FOR A SET OF PATTERNS 24 3 ANSWERING RANGE MINIMUM QUERIES IN CONSTANT TIME 33 3.1 BASIC DEFINITIONS 33 3.2 RANGE MINIMUM VS. LOWEST COMMON ANCESTOR 34 3.3 RANGE MINIMUM QUERIES 42 3.3.1 THE SPARSE TABLE ALGORITHM 42 3.3.2 AN OPTIMAL ALGORITHM 43 3.4 COMPLETING THE PROOF OF CORRECTNESS 53 4 ENHANCED SUFFIX ARRAYS 59 4.1 SUFFIX ARRAYS 59 4.1.1 LINEAR-TIME CONSTRUCTION 61 4.1.2 INDUCED SORTING 68 4.2 THE LCP-ARRAY 79 4.2.1 LINEAR-TIME CONSTRUCTION 79 4.2.2 LONGEST COMMON PREFIX 84 4.3 THE LCP-INTERVAL TREE 85 4.3.1 FINDING CHILD AND PARENT INTERVALS . 88 4.3.2 BOTTOM-UP TRAVERSAL 93 4.3.3 TOP-DOWN TRAVERSAL 98 HTTP://D-NB.INFO/1041812140 VILL CONTENTS 4.3.4 FINDING CHILD INTERVALS WITHOUT RMQS 105 4.4 SUFFIX TREES 110 4.4.1 LINEAR-TIME CONSTRUCTION 113 5 APPLICATIONS OF ENHANCED SUFFIX ARRAYS 115 5.1 EXACT STRING MATCHING 116 5.1.1 FORWARD SEARCH ON SUFFIX TREES 116 5.1.2 FORWARD SEARCH ON SUFFIX ARRAYS 117 5.1.3 BINARY SEARCH 120 5.2 LEMPEL-ZIV FACTORIZATION 125 5.2.1 LONGEST PREVIOUS SUBSTRING 126 5.2.2 ULTRA-FAST FACTORIZATION 134 5.3 FINDING REPEATS 138 5.3.1 LONGEST REPEATS 140 5.3.2 SUPERMAXIMAL REPEATS 144 5.3.3 MAXIMAL REPEATS 148 5.3.4 MAXIMAL REPEATED PAIRS 149 5.3.5 NON-OVERLAPPING REPEATS 155 5.3.6 MAXIMAL PERIODICITIES 157 5.4 COMPARING TWO STRINGS 173 5.4.1 GENERALIZED SUFFIX ARRAY 173 5.4.2 LONGEST COMMON SUBSTRING 181 5.4.3 FINDING EXACT MATCHES 183 5.5 TRAVERSALS WITH SUFFIX LINKS 185 5.5.1 SUFFIX LINKS IN THE SUFFIX TREE 185 5.5.2 SUFFIX LINKS IN THE LCP-INTERVAL TREE 186 5.5.3 COMPUTING SUFFIX LINKS SPACE EFFICIENTLY 187 5.5.4 MATCHING STATISTICS 194 5.5.5 MERGING TWO SUFFIX ARRAYS IN LINEAR TIME 203 5.6 COMPARING MULTIPLE STRINGS .... - 206 5.6.1 GENERALIZED SUFFIX ARRAY 206 5.6.2 LONGEST COMMON SUBSTRING 208 5.6.3 DOCUMENT FREQUENCY 216 5.6.4 DOCUMENT RETRIEVAL 221 5.6.5 SHORTEST UNIQUE SUBSTRINGS 224 5.6.6 A DISTANCE MEASURE FOR GENOMES 228 5.6.7 ALL-PAIRS SUFFIX-PREFIX MATCHING 231 5.7 STRING KERNELS 237 5.7.1 MACHINE LEARNING 237 5.7.2 CALCULATING A STRING KERNEL 238 5.7.3 CALCULATING THE KERNEL MATRIX 243 5.7.4 CLASSIFICATION 243 5.7.5 THE TF-IDF WEIGHTING SCHEME 244 CONTENTS IX 5.8 STRING MINING 247 5.8.1 EXTRACTION PHASE 248 5.8.2 INTERSECTION PHASE 250 6 MAKING THE COMPONENTS OF ENHANCED SUFFIX ARRAYS SMALLER 257 6.1 CONSTANT TIME RANK AND SELECT QUERIES 257 6.2 COMPRESSED SUFFIX AND LCP-ARRAYS 262 6.2.1 COMPRESSED SUFFIX ARRAY 262 6.2.2 COMPRESSED LCP-ARRAY 264 6.3 THE BALANCED PARENTHESES SEQUENCE OF THE LCP-ARRAY . . . 265 6.3.1 FINDING THE PARENT INTERVAL 270 6.3.2 FINDING CHILD INTERVALS 272 6.3.3 COMPUTING GETLNTERVAL([I..J],C) 274 6.3.4 ANSWERING RMQS IN CONSTANT TIME 275 6.3.5 COMPUTING SUFFIX LINK INTERVALS 276 6.3.6 ATTACHING ADDITIONAL INFORMATION 276 7 COMPRESSED FULL-TEXT INDEXES 281 7.1 THE COMPONENTS OF A COMPRESSED FULL-TEXT INDEX 281 7.2 THE BURROWS-WHEELER TRANSFORM 282 7.2.1 ENCODING 282 7.2.2 DECODING 284 7.2.3 DATA COMPRESSION 287 7.2.4 DIRECT CONSTRUCTION OF THE BWT 291 7.3 BACKWARD SEARCH 299 7.3.1 A SIMPLE FM-INDEX 299 7.3.2 THE SEARCH ALGORITHM 300 7.4 WAVELET TREES 303 7.4.1 ANSWERING RANK AND SELECT QUERIES 304 7.4.2 RETRIEVAL OF SA [I] AND THE STRING STARTING AT SA [I] . . 306 7.4.3 IMPLEMENTATION: IF A IS A POWER OF 2 307 7.4.4 IMPLEMENTATION: IF A IS NOT A POWER OF 2 310 7.4.5 OTHER TYPES OF WAVELET TREES 315 7.5 ANALYZING A STRING SPACE EFFICIENTLY 315 7.5.1 CONSTRUCTION OF THE LCP-ARRAY FROM THE BWT . . . . 315 7.5.2 BOTTOM-UP TRAVERSAL OF THE LCP-INTERVAL TREE .... 321 7.5.3 SHORTEST UNIQUE SUBSTRINGS 322 7.5.4 TOP-DOWN TRAVERSAL OF THE LCP-INTERVAL TREE 323 7.5.5 FINDING REPEATS 328 7.5.6 LEMPEL-ZIV FACTORIZATION 332 7.6 SPACE-EFFICIENT COMPARISON OF TWO STRINGS 336 7.6.1 MATCHING STATISTICS 336 7.6.2 MAXIMAL EXACT MATCHES 340 7.6.3 MERGING BURROWS-WHEELER TRANSFORMED STRINGS . . 342 X CONTENTS 7.7 SPACE-EFFICIENT COMPARISON OF MULTIPLE STRINGS 345 7.7.1 DOCUMENT ARRAY, LCP-ARRAY, AND CORRECTION TERMS 345 7.7.2 DOCUMENT RETRIEVAL WITH WAVELET TREES 348 7.7.3 ALL-PAIRS SUFFIX-PREFIX MATCHING 352 7.8 BIDIRECTIONAL SEARCH 357 7.8.1 BURROWS-WHEELER TRANSFORM OF THE REVERSE STRING . 358 7.8.2 THE SUFFIX ARRAY OF THE REVERSE STRING 364 7.8.3 THE LCP-ARRAY OF THE REVERSE STRING 366 7.8.4 THE BIDIRECTIONAL SEARCH ALGORITHM 369 7.9 APPROXIMATE STRING MATCHING 374 7.9.1 USING BACKWARD SEARCH 375 7.9.2 USING BIDIRECTIONAL SEARCH 380 8 SEQUENCE ALIGNMENT 385 8.1 PAIRWISE ALIGNMENT 386 8.1.1 DISTANCE METHODS 387 8.1.2 COMPUTING AN OPTIMAL ALIGNMENT IN LINEAR SPACE . 393 8.1.3 EDIT DISTANCE 398 8.1.4 SIMILARITY METHODS 399 8.1.5 DISTANCE VS. SIMILARITY 401 8.1.6 GENERAL SIMILARITY FUNCTIONS AND GAP PENALTIES . . 402 8.2 MULTIPLE ALIGNMENT 406 8.2.1 PRUNING THE SEARCH SPACE 409 8.2.2 A 2-APPROXIMATION ALGORITHM 411 8.2.3 PROGRESSIVE ALIGNMENT 415 8.3 WHOLE GENOME ALIGNMENT 417 8.3.1 BASIC DEFINITIONS AND CONCEPTS 418 8.3.2 A GLOBAL CHAINING ALGORITHM 420 8.3.3 ALTERNATIVE DATA STRUCTURES 423 8.3.4 LONGEST/HEAVIEST INCREASING SUBSEQUENCE 424 9 SORTING BY REVERSALS 429 9.1 INTRODUCTION 429 9.2 BASIC DEFINITIONS 437 9.3 THE REALITY-DESIRE DIAGRAM 440 9.4 COMPONENTS 445 9.4.1 ELEMENTARY INTERVALS 445 9.4.2 FINDING CYCLES AND COMPONENTS 448 9.5 SORTING A PERMUTATION WITHOUT BAD COMPONENTS 451 9.6 DEALING WITH BAD COMPONENTS 455 9.6.1 HURDLES 458 9.6.2 A FORTRESS 461 9.7 SORTING BY REVERSALS IN QUADRATIC TIME 467 9.7.1 FINDING A HAPPY CLIQUE 468 CONTENTS XL 9.7.2 SEARCHING THE HAPPY CLIQUE 473 10 PHYLOGENETIC RECONSTRUCTION 477 10.1 INTRODUCTION 477 10.1.1 METHODS OF PHYLOGENETIC INFERENCE 479 10.1.2 MOLECULAR ANTHROPOLOGY 481 10.2 BASIC DEFINITIONS 489 10.3 ULTRAMETRIC DISTANCE MATRICES AND TREES 492 10.3.1 CHARACTERIZATION OF ULTRAMETRIC MATRICES 494 10.3.2 CONSTRUCTION ALGORITHM 497 10.3.3 THE UPGMA-ALGORITHM 501 10.3.4 FAST UPGMA IMPLEMENTATION BASED ON QUADTREES 509 10.4 ADDITIVE DISTANCE MATRICES AND TREES 514 10.4.1 ULTRAMETRIC TREES REVISITED 515 10.4.2 REDUCTION OF THE ADDITIVE TREE PROBLEM 516 10.4.3 CHARACTERIZATION OF ADDITIVE MATRICES 521 10.4.4 CONSTRUCTION ALGORITHM 524 10.4.5 SPLITS AND QUARTETS 526 10.4.6 UNIQUENESS OF THE ADDITIVE TREE 528 10.5 NEIGHBOR-JOINING ALGORITHMS 531 10.5.1 FARRIS NEIGHBOR-JOINING ALGORITHM . 534 10.5.2 SAITOU AND NEI S NEIGHBOR-JOINING ALGORITHM .... 540 10.5.3 FAST NEIGHBOR-JOINING 546 10.6 NON-ADDITIVE DISSIMILARITY MATRICES 548 10.6.1 NEARLY ADDITIVE MATRICES AND QUARTET-CONSISTENCY . 549 10.6.2 ESTIMATING EDGE WEIGHTS 561 10.6.3 BOOTSTRAPPING 569 BIBLIOGRAPHY 571 INDEX 599
any_adam_object	1
author	Ohlebusch, Enno
author_facet	Ohlebusch, Enno
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author_sort	Ohlebusch, Enno
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building	Verbundindex
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classification_rvk	WC 7700
ctrlnum	(OCoLC)859540039 (DE-599)DNB1041812140
dewey-full	570.285
dewey-hundreds	500 - Natural sciences and mathematics
dewey-ones	570 - Biology
dewey-raw	570.285
dewey-search	570.285
dewey-sort	3570.285
dewey-tens	570 - Biology
discipline	Biologie Informatik
format	Book
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isbn	9783000413162
language	English
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spelling	Ohlebusch, Enno Verfasser aut Bioinformatics algorithms sequence analysis, genome rearrangements, and phylogenetic reconstruction Enno Ohlebusch Ulm <<E.>> Ohlebusch 2013 XVI, 604 S. graph. Darst. 24 cm txt rdacontent n rdamedia nc rdacarrier Literaturangaben DNB Datenaustausch application/pdf http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=027231154&sequence=000001&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA Inhaltsverzeichnis
spellingShingle	Ohlebusch, Enno Bioinformatics algorithms sequence analysis, genome rearrangements, and phylogenetic reconstruction
title	Bioinformatics algorithms sequence analysis, genome rearrangements, and phylogenetic reconstruction
title_auth	Bioinformatics algorithms sequence analysis, genome rearrangements, and phylogenetic reconstruction
title_exact_search	Bioinformatics algorithms sequence analysis, genome rearrangements, and phylogenetic reconstruction
title_full	Bioinformatics algorithms sequence analysis, genome rearrangements, and phylogenetic reconstruction Enno Ohlebusch
title_fullStr	Bioinformatics algorithms sequence analysis, genome rearrangements, and phylogenetic reconstruction Enno Ohlebusch
title_full_unstemmed	Bioinformatics algorithms sequence analysis, genome rearrangements, and phylogenetic reconstruction Enno Ohlebusch
title_short	Bioinformatics algorithms
title_sort	bioinformatics algorithms sequence analysis genome rearrangements and phylogenetic reconstruction
title_sub	sequence analysis, genome rearrangements, and phylogenetic reconstruction
url	http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=027231154&sequence=000001&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA
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