An easy to use web server for identifying regulatory RNA motifs and functional sites. Through its integrated user-friendly interface, user is capable of using various analytical approaches and observing results with graphical visualization conveniently.
Predicts iron-responsive elements in RNA or DNA sequences based on a sequence searcher Perl program. The SIREs web server uses a simple data input interface and provides structure analysis, predicted RNA folds, folding energy data and an overall quality flag based on properties of well characterized IREs. Results are reported in a tabular format and as a schematic visual representation that highlights important features of the IRE.
Estimates the concentration of gene expression codes in different non-coding parts of genes and transcripts, such as introns and untranslated regions. Chimera can be used for detecting and understanding gene expression codes in different parts of the genome/genes in previously un-studied organisms. The algorithm can be used for developing novel gene expression models and for gene expression engineering and synthetic biology systems.
Allows users to determine regulatory sequence elements from sets of co-regulated genes. RECIT is a web application with the aim of assisting in the integration and prioritization of elements for mechanistic laboratory-based experiments. The software is able to create visualizations. The platform accepts position-specific probability matrixes (PSPMs) from various element discovery software as well as outputs from BioProspector, Weeder, or RNAProfile software.
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