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Open Access Publications from the University of California

Scalable Online Algorithmic Biology Education and DCJ- Indel Sorting /

  • Author(s): Compeau, Phillip E. C.
  • et al.

We describe the concept of a Massive Adaptive Interactive Text (MAIT), a new generation of online learning experiences that can disrupt both large university courses and traditional published textbooks as well as facilitate "flipped" courses. We provide a sample of learning materials that we have begun developing into a MAIT in order to introduce the combinatorics of genome rearrangements. This expository introduction to genome rearrangements facilitates the transition toward research results based upon the computational problem of DCJ-indel sorting, which asks for the minimum number of double-cut- and-join operations (DCJs) in addition to the insertion/ deletion of chromosomes and chromosomal intervals (indels) required to transform one genome into another. We present a novel framework for DCJ-indel sorting, which allows us to classify the solution space of this problem. We then extend this framework to consider a generalized form of DCJ-indel sorting in which the cost of a DCJ is equal to 1 and the cost of an indel is any nonnegative constant, and we demand a minimum-cost collection of DCJs and indels transforming one genome into another. For genomes with circular chromosomes, we solve this generalized problem for any indel cost, thus resolving the open case in which the cost of an indel is larger than 1

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