Abstract
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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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. https://doi.org/10.1007/978-3-319-19048-8_20
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DOI: https://doi.org/10.1007/978-3-319-19048-8_20
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