Structure Prediction, Visualization, and Annotation

Contains links to applications for the visualization, prediction, and design of RNA molecules including siRNAs, secondary structure, and folding kinetics.

Found 85 links

Displaying 15 links

ARTSTool Content

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Alignment of RNA Tertiary Structures (ARTS) is a method for aligning two nucleic acid structures (RNAs or DNAs) and detecting a-priori unknown common substructures.

AsiDesignerTool Content

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AsiDesigner is a design software system for siRNA design, that takes into account alternative splicing for mRNA level gene silencing. The software also has the capacity to design siRNAs for silencing of multiple mRNAs simultaneously, to score the performance of designed siRNAs, to search for off-targets with BLAST and FASTA algorithms, and to check for secondary structure energy of siRNAs.

CARNATool Content

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CARNA is a web tool for multiple alignment of RNA molecules. CARNA requires only the RNA sequences as input and will compute base pair probability matrices and align the sequences based on their full ensembles of structures. Alternatively, you can also provide base pair probability matrices or FASTA alignments for your sequences.

links directory index: 0
TitlePublication YearGoogle Scholar Citation Count
CARNA--alignment of RNA structure ensembles.20120

CARNACTool Content

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Server which predicts conserved secondary structure elements of homologous RNAs. The input of a set of RNA sequences are not required to be previously aligned.

CentroidFoldTool Content

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Recognizing the growing role for non-coding RNAs (ncRNAs) in cells, the CentroidFold web server predicts RNA secondary structure from input sequence data (single or multiple alignments).

COGNACTool Content

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COGNAC: a webserver for searching and annotating hydrogen bonded base interactions in RNA 3-dimensional structures.

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TitlePublication YearGoogle Scholar Citation Count

CorreLogoTool Content

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CorreLogo generates a 3D sequence logo for RNA or DNA alignments. The first two dimensions of the sequence logo display information about the information content and residue composition of individual columns of the alignment. The 3D sequence logo consists of a square matrix that shows columns with high mutual information, a measure of how much the residues in two alignment columns are correlated.

CyloFoldTool Content

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CyloFold is a web tool for RNA secondary structure prediction that is not restricted in terms of pseudoknot complexity.

links directory index: 9
TitlePublication YearGoogle Scholar Citation Count
CyloFold: secondary structure prediction including pseudoknots20109

DEQORDatabase Content

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Tool which aids in the design and quality control of small interfering RNAs (siRNAs) for RNA interference (RNAi) and gene silencing. It evaluates the inhibitory potency of potential siRNA sequences as well as identifying gene regions that have a high silencing capacity.

e-RNATool Content

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eRNA is a collection of web servers for comparative RNA structure prediction and visualisation.

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TitlePublication YearGoogle Scholar Citation Count

E-RNAiTool Content

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E-RNAi is a tool for designing and evaluating dsRNA constructs suitable for RNAi experiments in 12 organisms including Drosophila, C. elegans, human and other emerging model organisms. E-RNAi also facilitates the design of secondary RNAi reagents for validation experiments, evaluation of pooled siRNA reagents and batch design.

ERPINTool Content

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ERPIN (Easy RNA Profile IdentificatioN) takes as input an RNA sequence alignment and secondary structure annotation and will identify a wide variety of known RNA motifs (such as tRNAs, 5S rRNAs, SRP RNA, C/D box snoRNAs, hammerhead motifs, miRNAs and others) in your sequence(s) of interest. Also contains tool for drawing secondary structure of motifs.

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