Biological Sequence Analysis Using the SeqAn C++ Library Chapman & Hall/CRC Computational Biology Series
Auteurs : Gogol-Döring Andreas, Reinert Knut
An Easy-to-Use Research Tool for Algorithm Testing and Development
Before the SeqAn project, there was clearly a lack of available implementations in sequence analysis, even for standard tasks. Implementations of needed algorithmic components were either unavailable or hard to access in third-party monolithic software products. Addressing these concerns, the developers of SeqAn created a comprehensive, easy-to-use, open source C++ library of efficient algorithms and data structures for the analysis of biological sequences. Written by the founders of this project, Biological Sequence Analysis Using the SeqAn C++ Library covers the SeqAn library, its documentation, and the supporting infrastructure.
The first part of the book describes the general library design. It introduces biological sequence analysis problems, discusses the benefit of using software libraries, summarizes the design principles and goals of SeqAn, details the main programming techniques used in SeqAn, and demonstrates the application of these techniques in various examples. Focusing on the components provided by SeqAn, the second part explores basic functionality, sequence data structures, alignments, pattern and motif searching, string indices, and graphs. The last part illustrates applications of SeqAn to genome alignment, consensus sequence in assembly projects, suffix array construction, and more.
This handy book describes a user-friendly library of efficient data types and algorithms for sequence analysis in computational biology. SeqAn enables not only the implementation of new algorithms, but also the sound analysis and comparison of existing algorithms.
VisitSeqAnfor more information.
The SeqAn Project. Library Contents. Applications. Bibliography. Index.
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.
Date de parution : 06-2017
15.6x23.4 cm
Date de parution : 11-2009
Ouvrage de 306 p.
15.6x23.4 cm
Thèmes de Biological Sequence Analysis Using the SeqAn C++ Library :
Mots-clés :
Biological Sequence Analysis; Suffix Arrays; Programming techniques; Needleman Wunsch Algorithm; The design in examples; Alignment Graphs; Aligning sequences with LAGAN; Int; Multiple alignment with segments; Template Argument; Basic statistical indices for SeqAn; Unsigned Int; Optimal Alignment; Sequences A1; Local Alignment; Suffix Trees; String Sets; Vice Versa; Algorithm Engineering; Sequence Analysis; Locality Sensitive Hashing; Memory Block; Graph Data Structures; Software Libraries; Edit Distance; String Indices; Standard Template Library; Running Time; Global Alignment; Biological Sequences