We develop efficient single- and multi-core algorithms to compute partition functions for RNA sequences. Our algorithms, which are based on McCaskill's algorithm, are benchmarked against state-of-the-art fast algorithms obtained using the parallelizing source-to-source compilers PLUTO and TRACO. On our Intel I9 computational platform, our best single core algorithm takes up to 81.2% less time than the single core algorithm resulting from PLUTO, which is faster than that obtained from TRACO. Our best multi-core algorithm takes up to 84.7% less time than the multi-core algorithm obtained using TRACO when run with 20 threads (our I9 has 10 cores and supports hyperthreading); the TRACO multi-core algorithm is faster than the PLUTO one.
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In this paper, we explain the development of a new Mizar tokenizer and parser program as a component of a search system that works on the Mizar Mathematical Library. The existing Mizar tokenizer and parser can handle only an article as a whole written in the Mizar language, however, the newly developed program can deal with a snippet of a Mizar article. In particular, since it is possible to handle a snippet of an article without specifying a vocabulary section of an environment part, it is expected that user input efforts will be greatly reduced.
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