%0 Journal Article
%T Riboswitch Detection Using Profile Hidden Markov Models
%A Payal Singh
%A Pradipta Bandyopadhyay
%A Sudha Bhattacharya
%A A Krishnamachari
%A Supratim Sengupta
%J BMC Bioinformatics
%D 2009
%I BioMed Central
%R 10.1186/1471-2105-10-325
%X Our method can detect riboswitches in genomic databases rapidly and accurately. Its sensitivity is comparable to the method based on the Covariance Model (CM). For six out of ten riboswitch classes, our method detects more than 99.5% of the candidates identified by the much slower CM method while being several hundred times faster. For three riboswitch classes, our method detects 97-99% of the candidates relative to the CM method. Our method works very well for those classes of riboswitches that are characterized by distinct and conserved sequence motifs.Riboswitches play a crucial role in controlling the expression of several prokaryotic genes involved in metabolism and transport processes. As more and more new classes of riboswitches are being discovered, it is important to understand the patterns of their intra and inter genomic distribution. Understanding such patterns will enable us to better understand the evolutionary history of these genetic regulatory elements. However, a complete picture of the distribution pattern of riboswitches will emerge only after accurate identification of riboswitches across genomes. We believe that the riboswitch detection method developed in this paper will aid in that process. The significant advantage in terms of speed, of our pHMM-based approach over the method based on CM allows us to scan entire databases (rather than 5'UTRs only) in a relatively short period of time in order to accurately identify riboswitch candidates.Recent discoveries of noncoding RNAs (ncRNAs), RNA molecules that do not code for proteins but function directly, reveal that they are abundant, widespread and perform truly diverse functions. [1,2] Significant and rapid advancements in RNA-mediated genetic control studies have established the importance of RNA in gene regulation [3,4]. The catalytic and regulatory roles of RNAs like ribozymes and riboswitches lend support to the hypothesis of RNA world and highlight the importance of RNA in the primordial wo
%U http://www.biomedcentral.com/1471-2105/10/325