Parallel Multiple Sequence Alignment with Decentralized Cache Support
In this paper we present a new method for aligning large sets of biological sequences. The method performs a sequence alignment in parallel and uses a decentralized cache to store intermediate results. The method allows alignments to be recomputed efficiently when new sequences are added or when alignments of different precisions are requested. Our method can be used to solve important biological problems like the adaptive update of a complete evolution tree when new sequences are added (without recomputing the whole tree).
To validate the method, some experiments were performed using up to 512 Small Subunit Ribosomal RNA sequences, which were analyzed with different levels of precision.
KeywordsMultiple Sequence Alignment Multiple Alignment Input Sequence Pairwise Alignment Cache Replacement
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- 2.Jiang, T., Lawler, E.L., Wang, L.: Aligning sequences via an evolutionary tree: complexity and approximation. In: ACM Symp. on Theory of Computing, pp. 760–769 (1994)Google Scholar
- 4.Guinand, F., Parmentier, G., Trystram, D.: Integration of multiple alignment and phylogeny reconstruction. In: Eur. Conf. on Comp. Biology, Poster Abstr (2002)Google Scholar
- 8.Mikhailov, D., Cofer, H., Gomperts, R.: Performance optimization of ClustalW: Parallel ClustalW, HT Clustal, and MULTICLUSTAL (2005), http://www.sgi.com/industries/sciences/chembio/resources/clustalw
- 9.Catalyurek, U., Ferreira, R., Kurc, T., Saltz, J.: Improving performance of multiple sequence alignment analysis in multi–client environments. In: Proc. of HiCOMB 2002 (2002)Google Scholar
- 11.Zola, J.: CaLi – generic computational buffers library (2005), http://icis.pcz.pl/~zola/CaLi