> Tag > Links tagged with 'nucleic acid conformation'

Links tagged with 'nucleic acid conformation'

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Found 72 links

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ReadOutTool Content

http://gibk26.bio.kyutech.ac.jp/jouhou/readout/ [open in a new window]

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DNA > Structure and Sequence Feature Detection
Expression > Gene Regulation
Protein > 3-D Structural Features

Readout is a server for the calculation of direct and indirect readout energy Z-scores which estimate the degree of sequence specificity of the protein-DNA complex. Readout can be useful for checking the quality of protein-DNA interactions in three dimensional (3D) structures.

links directory index: 318
TitlePublication YearGoogle Scholar Citation Count
ReadOut: structure-based calculation of direct and indirect readout energies and specificities for protein-DNA recognition200628
Intermolecular and intramolecular readout mechanisms in protein-DNA recognition200487
Specificity of protein-DNA recognition revealed by structure-based potentials: symmetric/asymmetric and cognate/non-cognate binding200262
Structure-based prediction of DNA target sites by regulatory proteins1999141
NAR Web Server Issue 2006
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tagsbacterial proteins base sequence binding sites biological models dimerization dna dna primers dna-binding proteins endonucleases gene expression regulation genetic promoter regions glucocorticoid receptors hydrogen bonding macromolecular substances metalloproteins molecular models nucleic acid conformation protein binding protein conformation protein kinases protein subunits proteins repressor proteins saccharomyces cerevisiae proteins tertiary protein structure thermodynamics type ii site-specific deoxyribonucleases viral proteins viral regulatory and accessory proteins water zinc fingers

RegRNATool Content

http://regrna.mbc.nctu.edu.tw/ [open in a new window]

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DNA > Structure and Sequence Feature Detection
Expression > Gene Regulation
Expression > Splicing
RNA > Functional RNAs
RNA > Motifs

Regulatory RNA (RegRNA) is a server for identifying regulatory RNA motifs and elements in mRNA sequences including: motifs located in the 5\'-UTR and 3\'-UTR; motifs involved in mRNA splicing and transcriptional regulation; other motifs in mRNA such as riboswitches and splice donor/acceptor sites; RNA structural features; and miRNA target sites.

links directory index: 59
TitlePublication YearGoogle Scholar Citation Count
RegRNA: an integrated web server for identifying regulatory RNA motifs and elements200659
NAR Web Server Issue 2006
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tagsanimals humans messenger rna mice nucleic acid conformation nucleic acid sequence homology rats ribonucleic acid regulatory sequences rna sequence analysis systems integration untranslated regions

RfamDatabase Content

http://rfam.sanger.ac.uk/ [open in a new window]

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RNA > Functional RNAs

Database of structure-annotated multiple sequence alignments, covariance models and family annotation for a number of non-coding RNA families.

links directory index: 1609
TitlePublication YearGoogle Scholar Citation Count
Rfam: Wikipedia, clans and the "decimal" release201154
Rfam: updates to the RNA families database2009282
Rfam: annotating non-coding RNAs in complete genomes2005705
Rfam: an RNA family database2003568
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external linksLink on Twitter Link on Wikipedia
tagsanimals base sequence encyclopedias as topic genome humans nucleic acid conformation nucleic acid databases rna rna sequence analysis sequence alignment statistical models untranslated rna

RfamDatabase Content

http://rfam.sanger.ac.uk [open in a new window]

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RNA > Databases

The Rfam database aims to catalogue non-coding RNAs through the use of sequence alignments and statistical profile models known as covariance models.

links directory index: 54
TitlePublication YearGoogle Scholar Citation Count
Rfam: Wikipedia, clans and the "decimal" release201154
NAR Database Issue 2011
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external linksLink on Twitter Link on Wikipedia
tagsencyclopedias as topic nucleic acid conformation nucleic acid databases rna sequence analysis sequence alignment statistical models untranslated rna

Riboswitch finderTool Content

http://riboswitch.bioapps.biozentrum.uni-wuerzburg.de/server.html [open in a new window]

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Expression > Gene Regulation
RNA > Motifs

RNA motif search program that identifies RNA motifs called riboswitches which are metabolic binding domains in mRNA that regulate gene expression. The program was originally designed around a set of riboswitches found in Bacillus subtilis.

links directory index: 39
TitlePublication YearGoogle Scholar Citation Count
Riboswitch finder--a tool for identification of riboswitch RNAs200439
NAR Web Server Issue 2004
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tagsallosteric regulation messenger rna nucleic acid conformation ribonucleic acid regulatory sequences rna sequence analysis

RNA AnalyzerTool Content

http://rnaanalyzer.bioapps.biozentrum.uni-wuerzburg.de/ [open in a new window]

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

RNA Analyzer searches for known structures and identifies RNA motifs in your input sequence.

links directory index: 28
TitlePublication YearGoogle Scholar Citation Count
A software tool-box for analysis of regulatory RNA elements200328
NAR Web Server Issue 2003
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tagscatalytic rna messenger rna nucleic acid conformation ribonucleic acid regulatory sequences rna sequence analysis

RNA MoviesTool Content

http://bibiserv.techfak.uni-bielefeld.de/rnamovies/ [open in a new window]

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RNA > Structure Prediction, Visualization, and Design

RNA Movies is a tool for the visualization of RNA secondary structure spaces. The program creates an interpolated animation of user provided sets of secondary structure data.

links directory index: 36
TitlePublication YearGoogle Scholar Citation Count
RNA Movies 2: sequential animation of RNA secondary structures20074
RNA movies: visualizing RNA secondary structure spaces199932
NAR Web Server Issue 2007
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tagsalgorithms bacterial rna computational biology computer simulation data display multimedia natronobacterium nucleic acid conformation programming languages rna

RNA StudioTool Content

http://bibiserv.techfak.uni-bielefeld.de/bibi/Tools_RNA_Studio.html [open in a new window]

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RNA > General Resources
RNA > Structure Prediction, Visualization, and Design

RNA Studio contains software for RNA analyses including tools for structure prediction, comparison, and visualization.

links directory index: 22
TitlePublication YearGoogle Scholar Citation Count
RNA-related tools on the Bielefeld Bioinformatics Server200322
NAR Web Server Issue 2003
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tagsbase sequence computational biology nucleic acid conformation rna

RNAborTool Content

http://bioinformatics.bc.edu/clotelab/RNAbor/ [open in a new window]

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RNA > Structure Prediction, Visualization, and Design

RNAbor is a server for computing structural neighbors of a RNA secondary structure.

links directory index: 4
TitlePublication YearGoogle Scholar Citation Count
RNAbor: a web server for RNA structural neighbors20074
NAR Web Server Issue 2007
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tagscluster analysis computational biology computer simulation conserved sequence genetic databases molecular sequence data nucleic acid conformation nucleic acid sequence homology ribonucleic acid regulatory sequences rna rna sequence analysis sequence alignment untranslated rna

RNAcontextTool Content

http://www.cs.toronto.edu/~hilal/rnacontext/ [open in a new window]

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Protein > 3-D Structural Features
Protein > Domains and Motifs

RNAcontext: a new motif-finding method designed to elucidate RNA-binding protein (RBP) specific sequence and structural preferences with greater accuracy than existing approahces.

links directory index: 9
TitlePublication YearGoogle Scholar Citation Count
RNAcontext: a new method for learning the sequence and structure binding preferences of RNA-binding proteins20109
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tagsalgorithms amino acid motifs amino acid sequence area under curve base sequence binding sites genetic models messenger rna nucleic acid conformation protein binding protein conformation protein databases rna-binding proteins statistical models
setsUniversity of Toronto

RNAhybridTool Content

http://bibiserv.techfak.uni-bielefeld.de/rnahybrid/ [open in a new window]

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Expression > Gene Regulation
RNA > Functional RNAs

RNAhybrid is a tool for predicting miRNA (microRNA) targets by calculating the minimum free energy of hybridization between target RNA and miRNA sequences.

links directory index: 748
TitlePublication YearGoogle Scholar Citation Count
RNAhybrid: microRNA target prediction easy, fast and flexible2006146
Fast and effective prediction of microRNA/target duplexes2004602
NAR Web Server Issue 2006
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tags3' untranslated regions algorithms animals binding sites body patterning caenorhabditis elegans caenorhabditis elegans proteins computational biology drosophila homeodomain proteins insect genes messenger rna micrornas nucleic acid conformation nucleic acid databases post-transcriptional rna processing rna interference thermodynamics

RNAmutantsTool Content

http://bioinformatics.bc.edu/clotelab/RNAmutants/ [open in a new window]

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RNA > Structure Prediction, Visualization, and Design

A web server to explore the effect of mutations on the RNA secondary structures.

links directory index: 5
TitlePublication YearGoogle Scholar Citation Count
RNAmutants: a web server to explore the mutational landscape of RNA secondary structures20095
NAR Web Server Issue 2009
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tagsnucleic acid conformation point mutation rna sequence analysis untranslated rna

RNAmuteTool Content

http://www.cs.bgu.ac.il/~xrnamute/XRNAmute [open in a new window]

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RNA > Structure Prediction, Visualization, and Design

RNAmute is a web server to facilitate mutational analysis of RNA secondary structures. Single point and multi-point mutations are handled.

links directory index: 4
TitlePublication YearGoogle Scholar Citation Count
The RNAmute web server for the mutational analysis of RNA secondary structures.20114
NAR Web Server Issue 2011
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tagsmutation nucleic acid conformation rna rna sequence analysis

RNAsoftTool Content

http://www.rnasoft.ca/ [open in a new window]

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RNA > Structure Prediction, Visualization, and Design

Software for RNA/DNA secondary structure prediction and design

links directory index: 155
TitlePublication YearGoogle Scholar Citation Count
A new algorithm for RNA secondary structure design200468
RNAsoft: A suite of RNA secondary structure prediction and design software tools200387
NAR Web Server Issue 2003
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tagsalgorithms base sequence computer simulation dna genetic databases genetic models molecular sequence data nucleic acid conformation rna

SARATool Content

http://sgu.bioinfo.cipf.es/services/SARA/ [open in a new window]

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Protein > 3-D Structure Comparison
RNA > Functional RNAs
RNA > Structure Prediction, Visualization, and Design

Based on the SARA program, the SARA server computes pairwise alignment of RNA structures for structure based assignment of RNA function. The server can also be used for RNA pairwise structure alignment.

This content is being maintained by marcius.

links directory index: 14
TitlePublication YearGoogle Scholar Citation Count
SARA: a server for function annotation of RNA structures200914
NAR Web Server Issue 2009
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tagsalgorithms nucleic acid conformation rna rna function prediction rna structure alignment

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