Profiling and Searching for RNA Pseudoknot Structures in Genomes
نویسندگان
چکیده
We developed a new method that can profile and efficiently search for pseudoknot structures in noncoding RNA genes. It profiles interleaving stems in pseudoknot structures with independent Covariance Model (CM) components. The statistical alignment score for searching is obtained by combining the alignment scores from all CM components. Our experiments show that the model can achieve excellent accuracy on both random and biological data. The efficiency achieved by the method makes it possible to search for structures that contain pseudoknot in genomes of a variety of organisms.
منابع مشابه
Fast and accurate search for non-coding RNA pseudoknot structures in genomes
MOTIVATION Searching genomes for non-coding RNAs (ncRNAs) by their secondary structure has become an important goal for bioinformatics. For pseudoknot-free structures, ncRNA search can be effective based on the covariance model and CYK-type dynamic programming. However, the computational difficulty in aligning an RNA sequence to a pseudoknot has prohibited fast and accurate search of arbitrary ...
متن کاملPseudoBase++: an extension of PseudoBase for easy searching, formatting and visualization of pseudoknots
Pseudoknots have been recognized to be an important type of RNA secondary structures responsible for many biological functions. PseudoBase, a widely used database of pseudoknot secondary structures developed at Leiden University, contains over 250 records of pseudoknots obtained in the past 25 years through crystallography, NMR, mutational experiments and sequence comparisons. To promptly addre...
متن کاملAn RNA Pseudoknot Folding Algorithm Based on Heuristic Searching
The general problem for the prediction of RNA secondary structure with pseudoknots is NP-hard. For a restricted class of pseudoknots, it was traditionally solved by the dynamic programming approach. However, these algorithms are computationally very expensive, when the input sequence or the contained pseudoknot is too long. We present a heuristic algorithm for RNA secondary structures with pseu...
متن کاملSpecies Specific DNA Profiling Mycobacterial Genomes Using Polymerase Chain Reaction with Single Universal Primer (UP-PCR)
Three tuberculous, twenty-one non-tuberculous mycobacterial (NTM) reference strains and seventy two isolates classified by biochemical tests were shown to produce specific sets of DNA fragments in a polymerase chain reaction with single universal primer (UP-PCR). A rather wide limit of tolerance for variations in procedure of PCR mixture preparation and thermocycling parameters was found. There...
متن کاملP-dcfold or How to Predict all Kinds of Pseudoknots in Rna Secondary Structures
Pseudoknots play important roles in many RNAs. But for computational reasons, pseudoknots are usually excluded from the definition of RNA secondary structures. Indeed, prediction of pseudoknots increase very highly the complexities in time of the algorithms, knowing that all existing algorithms for RNA secondary structure prediction have complexities at least of O(n). Some algorithms have been ...
متن کامل