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Computability of Models for Sequence Assembly

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Algorithms in Bioinformatics (WABI 2007)

Part of the book series: Lecture Notes in Computer Science ((LNBI,volume 4645))

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Abstract

Graph-theoretic models have come to the forefront as some of the most powerful and practical methods for sequence assembly. Simultaneously, the computational hardness of the underlying graph algorithms has remained open. Here we present two theoretical results about the complexity of these models for sequence assembly. In the first part, we show sequence assembly to be NP-hard under two different models: string graphs and de Bruijn graphs. Together with an earlier result on the NP-hardness of overlap graphs, this demonstrates that all of the popular graph-theoretic sequence assembly paradigms are NP-hard. In our second result, we give the first, to our knowledge, optimal polynomial time algorithm for genome assembly that explicitly models the double-strandedness of DNA. We solve the Chinese Postman Problem on bidirected graphs using bidirected flow techniques and show to how to use it to find the shortest double-stranded DNA sequence which contains a given set of k-long words. This algorithm has applications to sequencing by hybridization and short read assembly.

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Raffaele Giancarlo Sridhar Hannenhalli

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© 2007 Springer-Verlag Berlin Heidelberg

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Medvedev, P., Georgiou, K., Myers, G., Brudno, M. (2007). Computability of Models for Sequence Assembly. In: Giancarlo, R., Hannenhalli, S. (eds) Algorithms in Bioinformatics. WABI 2007. Lecture Notes in Computer Science(), vol 4645. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-540-74126-8_27

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  • DOI: https://doi.org/10.1007/978-3-540-74126-8_27

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-540-74125-1

  • Online ISBN: 978-3-540-74126-8

  • eBook Packages: Computer ScienceComputer Science (R0)

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