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This paper describes the message passing parallel implementation of the Cross Motif Search algorithm (MPI‐CMS). It is an extension and specifically improves on the results obtained in a conference paper presented at PBIO 2014. CMS is a bioinformatics algorithm whose goal is to search for geometrical motifs in proteins. For the purpose of a complete characterization of protein similarities, it would...
The retrieval and identification of geometrical motifs is an important open problem in bioinformatics. In previous works we presented Cross Motif Search (CMS), a novel algorithm which is able to search for recurring geometrical patterns in the secondary structure of proteins. A single run of CMS is able to look for similarities between a pair of proteins, and can be easily extended to compare each...
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