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Links tagged with 'rna'

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Found 71 links

Displaying 15 links

3VTool Content

http://3vee.molmovdb.org

Protein > 3-D Structural Features

The 3V web server extracts and analyzes all of the internal volumes from input RNA and protein structures. Output is volumetric representations in images and downloadable files.

NAR Web Server Issue 2010
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tagsbinding sites molecular models nucleic acid conformation protein conformation rna

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

Assembly PCR Oligo MakerTool Content

http://publish.yorku.ca/~pjohnson/AssemblyPCRoligomaker.html

DNA > Tools For the Bench

Assembly PCR Oligo Maker is a tool for designing oligodeoxynucleotides for the PCR based construction of long DNA molecules.

NAR Web Server Issue 2005
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tagsdna oligodeoxyribonucleotides polymerase chain reaction rna synthetic genes

Berkeley Drosophila Genome ProjectResource Content

http://www.fruitfly.org/

Model Organisms > Fly

Good entrez to fly genome resources.

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tagsamino acid sequence animals base sequence cell line cluster analysis complementary dna dna sequence analysis drosophila melanogaster expressed sequence tags gene library genetic databases genome insect genes male membrane glycoproteins membrane proteins molecular sequence data rna sequence alignment testis

BIND - The Biomolecular Interaction Network DatabaseDatabase Content

http://bond.unleashedinformatics.com/Action

Protein > Interactions, Pathways, Enzymes

Stores full descriptions of interactions, molecular complexes and pathways; researchers are able to submit new records.

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tagsamino acid sequence animals dna factual databases humans macromolecular substances molecular biology protein databases protein interaction mapping proteins rna sequence alignment statistical models tertiary protein structure

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

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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tagsnucleic acid conformation nucleic acid sequence homology rna rna sequence analysis

CLICKTool Content

http://mspc.bii.a-star.edu.sg/click

Protein > 3-D Structure Comparison

CLICK web server is a topology independent method of comparison of biomolecular 3D structures.

NAR Web Server Issue 2011
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tagsalgorithms molecular conformation molecular models nucleic acid conformation protein conformation rna

corRnaTool Content

http://corrna.cs.mcgill.ca

RNA > Functional RNAs

corRna is a web server for predicting the multiple point deleterious mutations in structural RNAs. Users can apply search heuristics to improve the quality of the predictions.

NAR Web Server Issue 2011
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tagsalgorithms mutagenesis mutation nucleic acid conformation rna

CPCTool Content

http://cpc.cbi.pku.edu.cn/programs/run_cpc.jsp

DNA > Gene Prediction
DNA > Structure and Sequence Feature Detection
RNA > Functional RNAs

CPC (Coding Potential Calculator) distinguishes protein-coding from non-coding RNAs based on the sequence features of the input transcripts.

NAR Web Server Issue 2007
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tagsanimals computational biology expressed sequence tags genetic code genetic transcription genetic variation genetic vectors messenger rna mice molecular sequence data nucleic acid databases protein biosynthesis proteins reproducibility of results 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

dbDEPCDatabase Content

http://lifecenter.sgst.cn/dbdepc/index.do

Human Genome > Databases
Protein > Databases

A database of differentially expressed proteins in human cancers (dbDEPC) collects curated cancer proteomics data, provides a resource for information on protein-level expression changes, and explores protein profile differences among different cancers. dbDEPC currently contains 1803 proteins differentially expressed in 15 cancers, curated from 65 mass spectrometry (MS) experiments in peer-reviewed publications.

NAR Database Issue 2010
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tagscomputational biology dna gene expression profiling genetic databases human genome humans neoplasms neoplastic gene expression regulation protein databases proteome 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

Ensembl Genome BrowserTool Content

http://www.ensembl.org/

DNA > Annotations
Human Genome > Annotations
Model Organisms > General Resources
Model Organisms > Other Organisms

Website, MySQL server and perl API access to software system which produces and maintains automatic annotation on eukaryotic genomes.

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tagsanimals bacterial genome base sequence cattle computational biology database management systems dna sequence analysis dogs fungal genome gene expression genetic databases genetic polymorphism genetic variation genome genomics human genome humans invertebrates mice nucleic acid databases nucleic acid regulatory sequences plant genome protein databases proteins rats reference standards rna sequence alignment species specificity synteny systems integration tertiary protein structure transcriptional regulatory elements