A Novel Heuristic for Local Multiple Alignment of Interspersed DNA Repeats
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Gapped extension for local multiple alignment of interspersed DNA repeats
ISBRA'08 Proceedings of the 4th international conference on Bioinformatics research and applications
Synthesising graphics card programs from DSLs
Proceedings of the 33rd ACM SIGPLAN conference on Programming Language Design and Implementation
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Summary: Hidden Markov models are widely applied within computational biology. The large data sets and complex models involved demand optimized implementations, while efficient exploration of model space requires rapid prototyping. These requirements are not met by existing solutions, and hand-coding is time-consuming and error-prone. Here, I present a compiler that takes over the mechanical process of implementing HMM algorithms, by translating high-level XML descriptions into efficient C++ implementations. The compiler is highly customizable, produces efficient and bug-free code, and includes several optimizations. Availability: http://genserv.anat.ox.ac.uk/software Contact: gerton.lunter@dpag.ox.ac.uk