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Diploid Alignments and Haplotyping

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Bioinformatics Research and Applications (ISBRA 2015)

Part of the book series: Lecture Notes in Computer Science ((LNBI,volume 9096))

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Sequence alignments have been studied for decades under the simplified model of a consensus sequence representing a chromosome. A natural question is if there is some more accurate notion of alignment for diploid (and in general, polyploid) organisms. We have developed such a notion in our recent work, but unfortunately the computational complexity remains open for such a diploid pair-wise alignment; only a trivial exponential algorithm is known that goes over all possible diploid alignments. In this paper, we shed some light on the complexity of diploid alignments by showing that a haplotyping version, involving three diploid inputs, is polynomial time solvable.

Partially supported by Academy of Finland under grant 284598 (CoECGR).

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Correspondence to Veli Mäkinen .

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Mäkinen, V., Valenzuela, D. (2015). Diploid Alignments and Haplotyping. In: Harrison, R., Li, Y., Măndoiu, I. (eds) Bioinformatics Research and Applications. ISBRA 2015. Lecture Notes in Computer Science(), vol 9096. Springer, Cham.

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  • Print ISBN: 978-3-319-19047-1

  • Online ISBN: 978-3-319-19048-8

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