title: SeqAn an efficient, generic C++ library for sequence analysis.
abstract: 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-of-the-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 different exact string matching algorithms. The second example is a simple version of the well-known MUMmer tool rewritten in SeqAn. Results indicate that our implementation is very efficient and versatile to use.
  
  
  CONCLUSIONS
  We anticipate that SeqAn greatly simplifies the rapid development of new bioinformatics tools by providing a collection of readily usable, well-designed algorithmic components which are fundamental for the field of sequence analysis. This leverages not only the implementation of new algorithms, but also enables a sound analysis and comparison of existing algorithms.
authors.affiliation: Algorithmische Bioinformatik, Institut für Informatik, Takustr, 9, 14195 Berlin, Germany. doering@inf.fu-berlin.de
authors.forename: Andreas
authors.initials: A
authors.lastname: Döring
authors.forename: David
authors.initials: D
authors.lastname: Weese
authors.forename: Tobias
authors.initials: T
authors.lastname: Rausch
authors.forename: Knut
authors.initials: K
authors.lastname: Reinert
mesh_terms: D000465:Algorithms; D003628:Database Management Systems; D030541:Databases, Genetic; D011381:Programming Languages; D016415:Sequence Alignment / Q000379:methods*; D017421:Sequence Analysis / Q000379:methods*; D012984:Software; D014584:User-Computer Interface