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

BMC Bioinformatics
Andreas DöringKnut Reinert

Abstract

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. 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. We anticipate that SeqAn greatly simplifies the rapid developmen...Continue Reading

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Citations

Sep 13, 2013·Nature Communications·Klas Hatje, Martin Kollmar
Dec 21, 2011·Briefings in Functional Genomics·Hong C LeeDavid Edwards
Aug 12, 2008·Bioinformatics·Tobias RauschKnut Reinert
Mar 18, 2009·Bioinformatics·Cole TrapnellSteven L Salzberg
Aug 4, 2009·Bioinformatics·Carsten Kemena, Cedric Notredame
Nov 3, 2009·Bioinformatics·Anne-Katrin EmdeSilke R Sperling
Dec 15, 2010·Bioinformatics·Samuel V Angiuoli, Steven L Salzberg
Jul 21, 2012·Bioinformatics·Toshiro K Ohsumi, Mark L Borowsky
Aug 28, 2012·Bioinformatics·David WeeseKnut Reinert
Jun 6, 2013·Bioinformatics·Alexei Nordell MarkovitsNicolas Gevry
Dec 27, 2011·Nucleic Acids Research·Athena AhmadiXiaohui Xie
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May 28, 2011·BMC Bioinformatics·Manuel HoltgreweKnut Reinert
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Oct 8, 2014·PeerJ·Johannes Köster, Sven Rahmann
Jul 17, 2014·Bioinformatics·Kathrin TrappeKnut Reinert

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Software Mentioned

Bio
Bioinformatics Template Library ( BTL )
MUMmer
Linux
Libcov
Windows Visual Studio
CGAL
NCBI C + + Toolkit
Sequence Class Library ( SCL )
Coffee

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