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High dimensional and high-resolution gene expression data generated by the in situ hybridization (ISH) technique provides biologists a powerful tool to study gene functions. Nevertheless, a major challenge in analyzing such data is how to efficiently retrieve genes showing certain spatial expression patterns and/or genes showing similar expression patterns as the query gene. The development of a fast...
In this paper, we presented a method to improve structural modeling based on conserved domain clusters and structure-anchored alignment. First we mapped all the InterPro domains in the entire PDB, partitioned and clustered homologous domains into the domain-based template library. This aimed at expanding structural coverage to more protein sequences. For each cluster, we generated a multiple structural...
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...
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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