HomoStRscan (Homologous Structural RNA Scan): A program for discovering homologous RNAs in complete genomes by taking a single RNA sequence with its secondary structure.
Our method completely differs from other currently used search algorithms of homologous structures or structural motifs in two important aspects: first, it takes account of information of both the primary sequence and the secondary structural constraints of the query RNA in detail including each base-pairs in the duplexes and each nucleotide in the single strands; second, the homologous RNA structures are strictly inferred from a robust statistical distribution of a quantitative measure, maximal similarity score of RNA structures.
HomoStRscan provides a flexible, robust and fine search tool for any homologous structural RNAs. The program is based on the structure matching, structure comparison and dynamic programming algorithm. It is implemented in the C programming language and running on Unix.
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