Coverart for item
The Resource Algorithms for next-generation sequencing data : techniques, approaches, and applications, Mourad Elloumi, editor, (electronic book)

Algorithms for next-generation sequencing data : techniques, approaches, and applications, Mourad Elloumi, editor, (electronic book)

Label
Algorithms for next-generation sequencing data : techniques, approaches, and applications
Title
Algorithms for next-generation sequencing data
Title remainder
techniques, approaches, and applications
Statement of responsibility
Mourad Elloumi, editor
Contributor
Editor
Subject
Language
eng
Summary
"The 14 contributed chapters in this book survey the most recent developments in high-performance algorithms for NGS data, offering fundamental insights and technical information specifically on indexing, compression and storage; error correction; alignment; and assembly."--
Member of
Assigning source
Provided by publisher
Cataloging source
YDX
Dewey number
572.8/633
Index
no index present
LC call number
QP625.N89
Literary form
non fiction
Nature of contents
  • dictionaries
  • bibliography
http://library.link/vocab/relatedWorkOrContributorName
Elloumi, Mourad
http://library.link/vocab/subjectName
  • Nucleotide sequence
  • Computer algorithms
Label
Algorithms for next-generation sequencing data : techniques, approaches, and applications, Mourad Elloumi, editor, (electronic book)
Instantiates
Publication
Copyright
Bibliography note
Includes bibliographical references
Carrier category
online resource
Carrier category code
cr
Carrier MARC source
rdacarrier
Content category
text
Content type code
txt
Content type MARC source
rdacontent
Contents
  • Preface; Contents; Contributors; Part I Indexing, Compression, and Storage of NGS Data; 1 Algorithms for Indexing Highly Similar DNA Sequences; 1.1 Introduction; 1.2 Basic Concepts; 1.3 Basic Data Structures; 1.3.1 Trie; 1.3.1.1 Structure Construction; 1.3.1.2 Search for a Pattern P of Length m; 1.3.2 Suffix Tree; 1.3.2.1 Structure Construction; 1.3.2.2 Search for a Pattern P of Length m; 1.3.3 DAWG; 1.3.3.1 Structure Construction; 1.3.3.2 Search for a Pattern P of Length m; 1.3.4 Suffix Array; 1.3.4.1 Structure Construction; 1.3.4.2 Search for a Pattern P of Length m
  • 1.4 Advanced Data Structures1.4.1 FM Index; 1.4.1.1 Burrows-Wheeler Transform; 1.4.1.2 Backward Search; 1.4.2 Compressed Suffix Array ; 1.4.2.1 Grossi-CSA; 1.4.2.2 Sadakane-CSA; 1.4.2.3 Grossi-Gupta-CSA; 1.4.3 Lempel-Ziv Indexes; 1.4.3.1 LZ78 Algorithm; 1.4.3.2 LZ Index; 1.5 More Advanced Data Structures; 1.5.1 Common and Differentiating Segments; 1.5.1.1 Model 1; 1.5.1.2 Model 2; 1.5.1.3 A Second Solution; 1.5.2 Fast Relative Lempel-Ziv Self-index; 1.5.3 BIO-FMI Index; 1.5.3.1 Description; 1.5.4 Suffix Tree of an Alignment; 1.5.4.1 Structure Construction
  • 1.5.4.2 Search for a Pattern P of Length m1.5.5 Suffix Array of an Alignment; 1.5.5.1 Structure Construction; 1.5.5.2 Search for a Pattern P of Length m; 1.6 Conclusion; References; 2 Full-Text Indexes for High-Throughput Sequencing; 2.1 Introduction; 2.1.1 Notations; 2.1.2 Padding; 2.2 Background; 2.2.1 Suffix Trie; 2.2.2 Suffix Tree; 2.2.3 Suffix Array; 2.2.4 Burrows-Wheeler Transform; 2.2.4.1 Inversion; 2.3 Suffix Trie Realizations; 2.3.1 Suffix Array; 2.3.2 FM-Index; 2.3.2.1 Rank Dictionaries; 2.3.2.2 Top-Down Traversal; 2.3.2.3 Sparse Suffix Array; 2.4 Suffix Tree Realizations
  • 2.4.1 Enhanced Suffix Array2.4.1.1 LCP Table; 2.4.1.2 Child Table; 2.4.1.3 Top-Down Traversal; 2.4.2 Lazy Suffix Tree; 2.4.2.1 The WOTD Algorithm; 2.4.2.2 The Data Structure; 2.4.2.3 Node Expansion; 2.4.2.4 Generalization to Multiple Sequences; 2.5 q-Gram Index Realizations; 2.5.1 Direct Addressing; 2.5.2 Open Addressing; 2.6 Applications; 2.6.1 Depth-First Traversal; 2.6.2 Exact String matching; 2.6.3 Approximate String Matching; 2.7 Conclusion; References; 3 Searching and Indexing Circular Patterns; 3.1 Introduction; 3.2 Circular Dictionary Matching
  • 3.2.1 Properties of the Partitioning Technique3.2.2 Circular String Matching via Filtering; 3.2.2.1 Longest Common Extension; 3.2.2.2 Algorithm CSMF; 3.2.2.3 Algorithm CSMF-Simple; 3.2.3 Circular Dictionary Matching via Filtering; 3.2.4 Key Results; 3.3 Circular Pattern Indexing; 3.3.1 The CPI-II Data Structure; 3.3.2 A Folklore Indexing Data Structure; 3.3.3 Key Results; 3.4 Final Remarks and Outlook; References; 4 De Novo NGS Data Compression; 4.1 Introduction; 4.2 Generic Text Compression; 4.2.1 Coding; 4.2.2 Modeling; 4.2.2.1 Basic Modeling; 4.2.2.2 Statistical-Based Approach
Dimensions
unknown
Extent
1 online resource.
Form of item
online
Isbn
9783319598246
Media category
computer
Media MARC source
rdamedia
Media type code
c
Specific material designation
remote
System control number
on1004597943
Label
Algorithms for next-generation sequencing data : techniques, approaches, and applications, Mourad Elloumi, editor, (electronic book)
Publication
Copyright
Bibliography note
Includes bibliographical references
Carrier category
online resource
Carrier category code
cr
Carrier MARC source
rdacarrier
Content category
text
Content type code
txt
Content type MARC source
rdacontent
Contents
  • Preface; Contents; Contributors; Part I Indexing, Compression, and Storage of NGS Data; 1 Algorithms for Indexing Highly Similar DNA Sequences; 1.1 Introduction; 1.2 Basic Concepts; 1.3 Basic Data Structures; 1.3.1 Trie; 1.3.1.1 Structure Construction; 1.3.1.2 Search for a Pattern P of Length m; 1.3.2 Suffix Tree; 1.3.2.1 Structure Construction; 1.3.2.2 Search for a Pattern P of Length m; 1.3.3 DAWG; 1.3.3.1 Structure Construction; 1.3.3.2 Search for a Pattern P of Length m; 1.3.4 Suffix Array; 1.3.4.1 Structure Construction; 1.3.4.2 Search for a Pattern P of Length m
  • 1.4 Advanced Data Structures1.4.1 FM Index; 1.4.1.1 Burrows-Wheeler Transform; 1.4.1.2 Backward Search; 1.4.2 Compressed Suffix Array ; 1.4.2.1 Grossi-CSA; 1.4.2.2 Sadakane-CSA; 1.4.2.3 Grossi-Gupta-CSA; 1.4.3 Lempel-Ziv Indexes; 1.4.3.1 LZ78 Algorithm; 1.4.3.2 LZ Index; 1.5 More Advanced Data Structures; 1.5.1 Common and Differentiating Segments; 1.5.1.1 Model 1; 1.5.1.2 Model 2; 1.5.1.3 A Second Solution; 1.5.2 Fast Relative Lempel-Ziv Self-index; 1.5.3 BIO-FMI Index; 1.5.3.1 Description; 1.5.4 Suffix Tree of an Alignment; 1.5.4.1 Structure Construction
  • 1.5.4.2 Search for a Pattern P of Length m1.5.5 Suffix Array of an Alignment; 1.5.5.1 Structure Construction; 1.5.5.2 Search for a Pattern P of Length m; 1.6 Conclusion; References; 2 Full-Text Indexes for High-Throughput Sequencing; 2.1 Introduction; 2.1.1 Notations; 2.1.2 Padding; 2.2 Background; 2.2.1 Suffix Trie; 2.2.2 Suffix Tree; 2.2.3 Suffix Array; 2.2.4 Burrows-Wheeler Transform; 2.2.4.1 Inversion; 2.3 Suffix Trie Realizations; 2.3.1 Suffix Array; 2.3.2 FM-Index; 2.3.2.1 Rank Dictionaries; 2.3.2.2 Top-Down Traversal; 2.3.2.3 Sparse Suffix Array; 2.4 Suffix Tree Realizations
  • 2.4.1 Enhanced Suffix Array2.4.1.1 LCP Table; 2.4.1.2 Child Table; 2.4.1.3 Top-Down Traversal; 2.4.2 Lazy Suffix Tree; 2.4.2.1 The WOTD Algorithm; 2.4.2.2 The Data Structure; 2.4.2.3 Node Expansion; 2.4.2.4 Generalization to Multiple Sequences; 2.5 q-Gram Index Realizations; 2.5.1 Direct Addressing; 2.5.2 Open Addressing; 2.6 Applications; 2.6.1 Depth-First Traversal; 2.6.2 Exact String matching; 2.6.3 Approximate String Matching; 2.7 Conclusion; References; 3 Searching and Indexing Circular Patterns; 3.1 Introduction; 3.2 Circular Dictionary Matching
  • 3.2.1 Properties of the Partitioning Technique3.2.2 Circular String Matching via Filtering; 3.2.2.1 Longest Common Extension; 3.2.2.2 Algorithm CSMF; 3.2.2.3 Algorithm CSMF-Simple; 3.2.3 Circular Dictionary Matching via Filtering; 3.2.4 Key Results; 3.3 Circular Pattern Indexing; 3.3.1 The CPI-II Data Structure; 3.3.2 A Folklore Indexing Data Structure; 3.3.3 Key Results; 3.4 Final Remarks and Outlook; References; 4 De Novo NGS Data Compression; 4.1 Introduction; 4.2 Generic Text Compression; 4.2.1 Coding; 4.2.2 Modeling; 4.2.2.1 Basic Modeling; 4.2.2.2 Statistical-Based Approach
Dimensions
unknown
Extent
1 online resource.
Form of item
online
Isbn
9783319598246
Media category
computer
Media MARC source
rdamedia
Media type code
c
Specific material designation
remote
System control number
on1004597943

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