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Bioinformatics Algorithms

Exploding Newspapers

Explore the fundamentals of genome assembly by understanding the Newspaper Problem analogy. Learn how short overlapping DNA sequences, or reads, are pieced together computationally to reconstruct entire genomes despite missing information and sequencing limits.

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The newspaper problem

Imagine that we stack a hundred copies of the June 27, 2000 edition of the New York Times on a pile of dynamite, and then we light the fuse. We ask you to further suspend your disbelief and assume that the newspapers are not all incinerated but instead explode cartoonishly into smoldering pieces of confetti. How could we use the tiny snippets of newspaper to figure out what the news was on June 27, 2000? We’ll call this crazy conundrum the Newspaper Problem (see figure below).

Don’t try this at home! Crazy as it may seem, the Newspaper Problem serves as an analogy for the computational framework of genome assembly.
Don’t try this at home! Crazy as it may seem, the Newspaper Problem serves as an analogy for the computational framework of genome assembly.

The Newspaper Problem is even more difficult than it may seem. Because we had multiple copies of the same edition of the newspaper, and because we undoubtedly lost some information in ...