Many combinatorial optimization problems in biosequence analysis are solved via dynamic programming. To increase programming productivity and program reliability, a domain specific language embedded in Haskell has been suggested. We point out several shortcomings of this approach, and report on some challenges in the (ongoing) project of migrating this domain specific language from its host language to a directly compiled implementation. Most of these challenges are domain specific optimizations, which not only improve significant constant factors of runtime and space requirements, but also affect asymptotic efficiency. We report on our solutions to some of these problems, and point out others that are still open.
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