Аннотация: RNA elements are known to regulate cell processes co- and post-transcriptionally. The functions of many regulatory RNA elements depend on their structure, so it is important to be able to determine the structure as well as to scan genomes for structured elements. Classic approaches to predict structured RNAs rely on DNA sequence analysis. There are two major types of information inferred from the sequence: thermodynamic stability of an RNA structure and evolutionary selection on base pair interactions. Last several years chemical probing of RNA as an alternative source of structural information gains popularity. There exist plenty of methods to integrate probing data into RNA secondary structure prediction algorithms. However, whether probing data could somehow contribute to detection of structured RNAs still remains open question. We previously developed energy-based approach RNASurface to detect locally optimal structured RNA elements. Now we integrate probing data into RNASurface energy model. We show that addition of experimental data allows better discrimination of ncRNAs from other transcripts. Application to genome-wide analysis with PARS data uncovers hundreds of previously undetectable segments, and some of them may be functional.

Аннотация: We analyze recently proposed multimedia digital fingerprint- ing codes and derive first results on a new arising combinatorial problem.