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Since comparative sequence analysis is effective for non-coding RNA detection and RNA secondary structure prediction, efficient computational methods are expected for structuraf alignment of RNA sequences. However, it is very difficuit to construct a weft structuraf afignment without knowing the secondary structures. In this paper, we present a new method for constructing structural alignment of RNA...
Comparative analysis of homologous sequences has been used to predict RNA secondary structure. However, most of existing comparative approaches are vulnerable to alignment errors and thus are not quite suitable for practical application. Here we devise a new method for predicting RNA secondary structure using multiple unaligned sequences. Our method completes the prediction in four major steps: 1)...
Recently, large-scale protein-protein interactions were recovered using the similar two-hybrid system for the model systems. This information allows us to investigate the protein interaction network from a systematic point of view. However, experimentally determined interactions are susceptible to errors. A previous assessment estimated that only ~10% of the interactions can be supported by more than...
In this paper, we present a fully automatic computational method to cluster orthologs and in-paralogs from multiple species. We use the program Blastp to generate a pairwise distance matrix, which is then normalized for each homologous group between and within the species included. We also used protein domains and their organization in protein sequences as an additional criterion for filtering false...
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