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Riboswitch Scanner

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Detects riboswitches from genomic sequences with high sensitivity and specificity. Riboswitch Scanner uses a method based on profile Hidden Markov Models (pHMMs) for detecting riboswitches. Riboswitch Scanner also provides the putative locations of the riboswitches in the genomic sequences. Riboswitch Scanner is able to detect 24 classes of riboswitches from complete genome sequences as well as from partial genome sequences.

PASIFIC / Prediction of Alternative Structures for Identification of Cis-regulation

Predicts whether this sequence can adopt two alternative structures conforming with the conditional termination paradigm. Combining machine learning with prediction of alternative RNA secondary structures, PASIFIC can detect riboswitches, attenuators and leaders in a manner not dependent on their sequence conservation in others species. PASIFIC is expected to assist in the identification of new riboswitches and attenuators in the bacterial pan-genome.

RibEx / Riboswitch Explorer

A web server capable of searching any sequence for known riboswitches as well as other predicted, but highly conserved, bacterial regulatory elements. RibEx allows the visual inspection of the identified motifs in relation to attenuators and open reading frames (ORFs). Any of the ORF's or regulatory elements' sequence can be obtained with a click and submitted to NCBI's BLAST. Alternatively, the genome context of all other genes regulated by the same element can be explored with our genome context tool (GeConT).

Riboswitch finder

A dedicated RNA motif search program and web server to identify RNA riboswitches. The Riboswitch finder analyses a given sequence using the web interface, checks specific sequence elements and secondary structure, calculates and displays the energy folding of the RNA structure and runs a number of tests including this information to determine whether high-sensitivity riboswitch motifs (or variants) according to the Bacillus subtilis type are present in the given RNA sequence.

RNAborMEA

Computes a maximum expected accuracy analogue Z(δ) of the Boltzmann partition function. RNAborMEA produces near-optimal structures that are closer to the biologically functional structures, in the case of conformational switches that are difficult to predict by any method. It also allows the user to stipulate (partial) hard constraints, that stipulate whether particular nucleotides are unpaired, or base-pair with certain other nucleotides. RNAborMEA produces strikingly different results from other software that produce suboptimal structures.