Biological Sequence Analysis Using the SeqAn C++ Library

Written by SeqAn project founders, this book describes the general library design of SeqAn. It introduces biological sequence analysis problems, discusses the benefit of using software libraries, summarizes SeqAn design principles and goals, details SeqAn programming techniques, and demonstrates the application of these techniques in various examples. Focusing on SeqAn components, the second part explores basic functionality, sequence data structures, alignments, pattern and motif searching, string indices, and graphs. The last part describes applications of SeqAn to genome alignment, consensus sequence, suffix array construction.