Biological Sequence Analysis Using the SeqAn C++ Library - Andreas Gogol-Döring

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Résumé :
The SeqAn project was initiated to offer quick access to the algorithms needed by researchers in computational biology and bioinformatics. A key to that invaluable resource, this book provides a highly accessible way for the rapid prototyping of algorithms in the field. For bioinformaticians, it serves as a guide for using algorithmic components already present in SeqAn. For expert programmers of C++ in sequence analysis, the book gives in-depth insight into the library's design principles and enables programmers to integrate their own algorithmic components into SeqAn. The library is available at www.seqan.de

Biographie:
Co-founder of the SeqAn project, Andreas Gogol-Doring works at the Max Delbruck 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 Universitat 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 Universitat Berlin in Germany.

Sommaire:
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