1st Edition
Biological Sequence Analysis Using the SeqAn C++ Library
THE SEQAN PROJECT
Background
Sequences in Bioinformatics
Sequence Analysis
Software Libraries
SeqAn
Design of SeqAn
Contents of SeqAn
Testing
Documentation
Distribution
Library Design
Design Overview
Design Goals
Programming Techniques
The C++ Programming Language
Generic Programming
Template Subclassing
Global Function Interfaces
Metafunctions
Further Techniques
The Design in Examples
Example 1: Value Counting
Example 2: Locality-Sensitive Hashing
LIBRARY CONTENTS
Basics
Containers and Values
Memory Allocation
Move Operations
Alphabets
Iterators
Conversions
Sequences
Strings
Overflow Strategies
String Specializations
Sequence Adaptors
Iterating Sequences
Sequence Modifiers
Segments
Comparators
String Sets
Sequence Conversion
File Input/Output
Alignments
Gaps Data Structures
Alignment Data Structures
Alignment Scoring
Alignment Problems Overview
Global Alignments
Chaining
Pattern Matching
Exact Searching
Exact Searching of Multiple Needles
Approximate Searching
Other Pattern Matching Problems
Motif Finding
Local Alignments
Seed-Based Motif Search
Multiple Sequence Motifs
Indices
Working with Indices
q-Gram Indices
Suffix Arrays
Enhanced Suffix Arrays
Graphs
Automata
Alignment Graphs
APPLICATIONS
Aligning Sequences with LAGAN
The LAGAN Algorithm
Implementation of LAGAN
Results
Multiple Alignment with Segments
The Algorithm
Implementation
Results
Basic Statistical Indices for SeqAn
Statistical Indices and Biological Sequence Analysis
Mathematical Outline
SeqAn Algorithms and Data Types
Implementation Outline
A BWT-Based Suffix Array Construction
Introduction to BWTWalk
The Main Idea of BWTWalk
Saving Space
SeqAn Implementation of BWTWalkFast
Containers with and without Fast Random Access
In-Place Version
Experiments
Conclusion
Bibliography
Index
Biography
Co-founder of the SeqAn project, Andreas Gogol-Döring works at the Max Delbrück Center for Molecular Medicine in Berlin, Germany. He was previously a research associate in the Algorithmic Bioinformatics group in the Department of Computer Science at Freie Universität Berlin in Germany.
Co-founder of the SeqAn project, Knut Reinert is a professor and head of the Algorithmic Bioinformatics group in the Department of Computer Science at Freie Universität Berlin in Germany.
