SeqAn An efficient, generic C++ library for sequence analysis

Background: The use of novel algorithmic techniques is pivotal to many important problems in life science. For example the sequencing of the human genome [1] would not have been possible without advanced assembly algorithms. However, owing to the high speed of technological progress and the urgent need for bioinformatics tools, there is a widening gap between state-ofthe-art algorithmic techniques and the actual algorithmic components of tools that are in widespread use. Results: To remedy this trend we propose the use of SeqAn, a library of efficient data types and algorithms for sequence analysis in computational biology. SeqAn comprises implementations of existing, practical state-of-the-art algorithmic components to provide a sound basis for algorithm testing and development. In this paper we describe the design and content of SeqAn and demonstrate its use by giving two examples. In the first example we show an application of SeqAn as an experimental platform by comparing differen...

• Type: Journal
• Year: 2008
• Where: BMCBI
• Authors: Andreas Döring, David Weese, Tobias Rausch, Knut Reinert
• Keywords: Algorithm, Algorithmic Components, Algorithmic Techniques, BMCBI 2008