DNA assembly from paired reads as 2-D jigsaw puzzles

Information Theory（2014）

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Abstract

We study the information theoretic limits of DNA assembly from paired reads. Each paired read consists of two subsequences of the DNA separated by a certain genomic distance. We show that this problem can be naturally cast as assembly of 2-D jigsaw puzzles. Using this representation, a necessary condition for assembly is derived and is shown to be nearly achieved on several probabilistic genome models.

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Key words

DNA,bioinformatics,genomics,2D jigsaw puzzles,DNA assembly information theoretic limits,DNA subsequences,genomic distance,paired reads,probabilistic genome models

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