Comparative Analysis of Cyclic Sequences: Viroids and other Small Circular RNAs
نویسندگان
چکیده
The analysis of small circular sequences requires specialized tools. While the differences between linear and circular sequences can be neglected in the case of long molecules such as bacterial genomes since in practice all analysis is performed in sequence windows, this is not true for viroids and related sequences which are usually only a few hundred basepairs long. In this contribution we present basic algorithms and corresponding software for circular RNAs. In particular, we discuss the problem of pairwise and multiple cyclic sequence alignments with affine gap costs, and an extension of a recent approach to circular RNA folding to the computation of consensus structures.
منابع مشابه
Prediction of Secondary Structure of Citrus Viroids Reported from Southern Iran
Abstract Viroids are smallest, single-stranded, circular, highly structured plant pathogenic RNAs that do not code for any protein. Viroids belong to two families, the Avsunviroidae and the Pospiviroidae. Members of the Pospiviroidae family adopt a rod-like secondary structure. In this study the most stable secondary structures of citrus viroid variants that reported from Fars province wer...
متن کاملSynthesis of infectious viroids and other circular RNAs.
Viroids are small autonomously replicating RNAs that share structural features with other subviral circular single-stranded RNAs of plants. Viroids and other circular single-stranded RNAs can be synthesised in vitro by a PCR-based procedure using a simple set of reactions. Two end-to-end primers are selected from a desired region of the viroid, one for the synthesis of the first strand cDNA and...
متن کاملPlant pathogenic RNAs and RNA catalysis.
The rolling circle replication of small circular plant pathogenic RNAs requires a processing step to convert multimeric intermediates to monomers which are then circularized. Eleven such RNAs are known so far, two are viroids, one is viroid-like and the remainder are satellite RNAs dependent on a helper virus for replication. The processing step is RNA-catalysed in all cases, at least in vitro....
متن کاملComparative sequence and structure of viroid-like RNAs of two plant viruses.
A newly discovered group of spherical plant viruses contains a bipartite genome consisting of a single-strand linear RNA molecule (RNA 1, Mr 1.5 x 10(6) ), and a single-strand, covalently closed circular viroid-like RNA molecule (RNA 2, Mr approximately 125,000). The nucleotide sequences of the RNA 2 of two of these, velvet tobacco mottle virus and solanum nodiflorum mottle virus, have been det...
متن کاملDiscovery of Replicating Circular RNAs by RNA-Seq and Computational Algorithms
Replicating circular RNAs are independent plant pathogens known as viroids, or act to modulate the pathogenesis of plant and animal viruses as their satellite RNAs. The rate of discovery of these subviral pathogens was low over the past 40 years because the classical approaches are technical demanding and time-consuming. We previously described an approach for homology-independent discovery of ...
متن کامل