The diploma thesis is dealing with searching in secondary structures of nucleic acids. The NA2Dsearch application was developed that allows to search databases of secondary structures for a structural motif. The application offers user-friendly graphical user interface where a query motif can be constructed in comfortable visual way using drag&drop, database and result structures can be browsed and visualized. The application contains original interactive nucleic acid structure visualization algorithm and novel search algorithm. The search algorithm can perform a motif search on structural data (unlike existing programs that can perform a motif search on sequence data). The motif search means that a query is created that describes the structure of motif of our interest with variabilities (e.g. the length of hairpin loop) that can be tolerated. Search results are ordered by the score computed according to the resemblance of hit and the query. The NA2Dsearch also supports searching in sequence data which are folded by external folding program. Searching capabilities are demonstrated on several search experiments involving HCV IRES and tRNA. Three searches for HCV IRES were performed: a search for HCV IRES structure in database of more than thousand of HCV genomic sequences, a folding analysis of HCV IRES...