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Riboswitch identification software tools | Gene expression data analysis

Riboswitches are short sequences of messenger RNA that can change their structural conformation to regulate the expression of adjacent genes. Computational prediction of putative riboswitches can provide direction to molecular biologists studying…
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Riboswitch…
Web

Riboswitch Scanner

Detects riboswitches from genomic sequences with high sensitivity and…

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.…

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PASIFIC
Web

PASIFIC Prediction of Alternative Structures for Identification of Cis-regulation

Predicts whether this sequence can adopt two alternative structures conforming…

Predicts whether this sequence can adopt two alternative structures conforming with the conditional termination paradigm. Combining machine learning with prediction of alternative RNA secondary…

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RibEx
Web

RibEx Riboswitch Explorer

A web server capable of searching any sequence for known riboswitches as well…

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…

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Riboswitch…
Web

Riboswitch finder

A dedicated RNA motif search program and web server to identify RNA…

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…

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DRD
Web

DRD Denison Riboswitch Detector

A Web-based tool for identifying putative riboswitches on a whole-genome scale.…

A Web-based tool for identifying putative riboswitches on a whole-genome scale. To efficiently identify high-quality strings of short conserved motifs, DRD transforms the problem into a heaviest path…

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RNAbor
Web

RNAbor

Computes the number and Boltzmann probability of the set of secondary…

Computes the number and Boltzmann probability of the set of secondary structures of a given RNA sequence at base pair distance δ from a given structure. The input structure could be the minimum free…

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RiboSW
Web

RiboSW

A tool for searching putative riboswitches. The efficiency of the proposed…

A tool for searching putative riboswitches. The efficiency of the proposed method for identifying riboswitches was improved in order to achieve a reasonable computational time required for the…

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RNAborMEA
Desktop

RNAborMEA

Computes a maximum expected accuracy analogue Z(δ) of the Boltzmann partition…

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…

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