> > Structure Prediction, Visualization, and Design

Structure Prediction, Visualization, and Design

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

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Found 61 links

Displaying 15 links

ARTSTool Content

http://bioinfo3d.cs.tau.ac.il/ARTS/

RNA > Structure Prediction, Visualization, and Design

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.

NAR Web Server Issue 2006
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tagsalgorithms base sequence chemical models computer simulation molecular models molecular sequence data nucleic acid conformation rna rna sequence analysis sequence alignment untranslated rna

AsiDesignerTool Content

http://sysbio.kribb.re.kr/AsiDesigner/

RNA > Structure Prediction, Visualization, and Design

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.

NAR Web Server Issue 2008
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tagsalgorithms alternative splicing messenger rna rna interference rna sequence analysis small interfering rna

CARNACTool Content

http://bioinfo.lifl.fr/carnac

RNA > Structure Prediction, Visualization, and Design

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.

NAR Web Server Issue 2004
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tagsalgorithms catalytic rna cytochromes endoribonucleases enterovirus genetic models messenger rna molecular sequence data nucleic acid conformation nucleic acid databases nucleic acid sequence homology ribonuclease p ribosomal rna rna rna sequence analysis sequence alignment statistical models telomerase viral rna

CentroidFoldTool Content

http://www.ncrna.org/centroidfold/

RNA > Structure Prediction, Visualization, and Design

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).

NAR Web Server Issue 2009
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tagsalgorithms nucleic acid conformation rna sequence analysis sequence alignment transfer rna untranslated rna

CentroidHomfold-LASTTool Content

http://www.ncrna.org/centroidhomfold/

RNA > Structure Prediction, Visualization, and Design

CentroidHomfold-LAST predicts the secondary structure of an RNA sequence using automatically collected homologous sequences.

NAR Web Server Issue 2011
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CorreLogoTool Content

http://correlogo.abcc.ncifcrf.gov/

RNA > Structure Prediction, Visualization, and Design
Sequence Comparison > Analysis of Aligned Sequences

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.

NAR Web Server Issue 2006
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tagsdna sequence analysis nucleic acid conformation ribosomal rna rna sequence analysis sequence alignment transfer rna

CyloFoldTool Content

http://cylofold.abcc.ncifcrf.gov/

RNA > Structure Prediction, Visualization, and Design

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

NAR Web Server Issue 2010
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tagsalgorithms nucleic acid conformation rna rna sequence analysis

DEQORDatabase Content

http://deqor.mpi-cbg.de/deqor_new/input.html

DNA > Tools For the Bench
Expression > Gene Regulation
RNA > Structure Prediction, Visualization, and Design

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.

NAR Web Server Issue 2004
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tagsrna interference small interfering rna

DIALTool Content

http://bioinformatics.bc.edu/clotelab/DIAL/

RNA > Motifs
RNA > Structure Prediction, Visualization, and Design

DIAL (dihedral alignment) is a server that provides access to a dynamic programming algorithm for structural alignment of RNA.

NAR Web Server Issue 2007
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tagsalgorithms base pairing computational biology nucleic acid conformation programming languages protein databases rna rna sequence analysis sequence alignment statistical models

DINAMeltTool Content

http://mfold.rna.albany.edu/?q=DINAMelt

DNA > Tools For the Bench
RNA > Structure Prediction, Visualization, and Design

DINAMelt is a tool for predicting hybridization and folding (secondary structure) of DNA and RNA using equilibrium thermodynamic methods.

NAR Web Server Issue 2005
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tagsalgorithms animals bacterial rna base sequence calorimetry dna dna sequence analysis fungal rna genetic hybridization introns molecular sequence data nucleic acid conformation nucleic acid denaturation nucleic acid hybridization oligonucleotides oligoribonucleotides phylogeny rats rna rna sequence analysis single-stranded dna structure-activity relationship temperature theoretical models transition temperature

E-RNAiTool Content

http://e-rnai.dkfz.de/

DNA > Tools For the Bench
Expression > Gene Regulation
Model Organisms > Fly
Model Organisms > Other Organisms
Model Organisms > Yeast
RNA > Structure Prediction, Visualization, and Design

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.

NAR Web Server Issue 2005NAR Web Server Issue 2010
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tagsanimals apoptosis caenorhabditis elegans cell cycle cell survival computational biology core binding factor alpha 2 subunit cultured cells dna primers dna-binding proteins double-stranded rna drosophila melanogaster drosophila proteins essential genes gene knockdown techniques genome genomic library genomics humans indicators and reagents inhibitor of apoptosis proteins insect genes phenotype proteome proto-oncogene proteins reproducibility of results rna interference rna sequence analysis sequence homology small interfering rna transcription factors

ERPINTool Content

http://tagc.univ-mrs.fr/erpin/

RNA > Motifs
RNA > Structure Prediction, Visualization, and Design

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.

NAR Web Server Issue 2004
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tagsalgorithms base sequence computational biology conserved sequence gene expression regulation iron nucleic acid conformation nucleic acid sequence homology response elements ribonucleic acid regulatory sequences ribosomal rna rna rna sequence analysis selenocysteine sensitivity and specificity sequence alignment transfer rna

FOLDALIGNTool Content

http://foldalign.ku.dk

RNA > Motifs
RNA > Structure Prediction, Visualization, and Design

FOLDALIGN is an algorithm for local simultaneous folding and aligning two or more RNA sequences.

NAR Web Server Issue 2005
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tagsalgorithms conserved sequence nucleic acid conformation nucleic acid sequence homology rna rna sequence analysis sequence alignment untranslated rna

IDT SciToolsTool Content

http://www.idtdna.com/SciTools/SciTools.aspx

DNA > Tools For the Bench
RNA > Structure Prediction, Visualization, and Design

IDT SciTools is a suite of online tools for the analysis and design of DNA and RNA oligomers. Tools include those for selection of PCR primers, antisense oligonucleotides, or sequences for RNA interference, as well as tools for calculation of secondary structures.

NAR Web Server Issue 2008
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tagsantisense oligonucleotides dna primers nucleic acid conformation oligonucleotide probes oligonucleotides small interfering rna

ILMTool Content

http://cic.cs.wustl.edu/RNA/

RNA > Structure Prediction, Visualization, and Design

Server which provides iterated loop matching and maximum weighted matching algorithms for pseudoknot containing RNA secondary structure prediction. Algorithms can apply thermodynamic and comparative information, and thus can be used for either aligned or individual sequences.

NAR Web Server Issue 2004
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tagsalgorithms bacillus subtilis bacterial rna base composition base pairing base sequence escherichia coli feedback molecular models molecular sequence data nucleic acid conformation nucleic acid sequence homology phylogeny reproducibility of results rna rna sequence analysis sensitivity and specificity sequence alignment theoretical models thermodynamics transfer rna

Tags associated with subcategory 'RNA/Structure Prediction, Visualization, and Design'

nucleic acid conformation rna algorithms rna sequence analysis base sequence molecular sequence data sequence alignment computational biology molecular models computer simulation oligonucleotides drug design antisense oligonucleotides binding sites sensitivity and specificity animals escherichia coli bayes theorem antisense rna rabbits phylogeny cricetinae drosophila gc rich sequence genetic vectors chick embryo cell line probability protozoan rna reproducibility of results ribosomal rna selenocysteine nucleic acid sequence homology protein databases molecular graphics molecular structure transcription factors sequence homology insect genes phenotype proteome proto-oncogene proteins protein protein conformation ribonucleic acid regulatory sequences luciferases base pairing feedback response elements iron structure validation three-dimensional imaging conserved sequence gene expression regulation green fluorescent proteins mammals nucleic acid repetitive sequences single-stranded dna dna sequence analysis nucleic acid hybridization nucleic acid denaturation tetrahymena thermophila xenopus laevis dna nucleic acid databases alzheimer disease amyloid beta-protein precursor transfer rna viral rna thermodynamics chemical models hiv reverse transcriptase genetic models base composition catalytic rna codon humans statistical models genetic databases messenger rna molecular cloning oligodeoxyribonucleotides plasmids luminescent proteins hela cells mice double-stranded rna gene silencing untranslated rna recombinant fusion proteins structure-activity relationship rna stability small interfering rna spliced leader rna statistical distributions viral proteins transfection temperature theoretical models transition temperature rna interference