Abstract
In this paper we present new approach to the problem of parallel multiple sequence alignment. The proposed method is based on the application of caching technique and is aimed to solve, with high precision, large alignment instances on the heterogeneous clusters. The cache is used to store partial alignment guiding trees which can be reused in future computations, and is applied to eliminate redundancy of computations in parallel environment. We describe an implementation based on the CaLi library, the software designed for caches implementation. We report preliminary experimental results and finally, we propose some extensions of our method.
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Keywords
- Multiple Sequence Alignment
- Multiple Alignment
- Distance Matrix
- Pairwise Alignment
- Neighborhood Determination
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Parmentier, G., Trystram, D., Zola, J. (2004). Cache-Based Parallelization of Multiple Sequence Alignment Problem. In: Danelutto, M., Vanneschi, M., Laforenza, D. (eds) Euro-Par 2004 Parallel Processing. Euro-Par 2004. Lecture Notes in Computer Science, vol 3149. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-540-27866-5_135
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DOI: https://doi.org/10.1007/978-3-540-27866-5_135
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