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Links tagged with 'small interfering rna'

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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

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

dsCheckTool Content

http://dscheck.rnai.jp/

DNA > Tools For the Bench
Expression > Gene Regulation

dsCheck takes a nucleotide sequence as input and estimates off-target effects caused by dsRNA (double-stranded RNA) employed in RNAi studies. dsCheck can be used either to verify previously designed dsRNA sequences, or to design off-target minimized dsRNAs.

NAR Web Server Issue 2005
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tagsalgorithms animals double-stranded rna rna interference rna sequence analysis small interfering rna

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

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

OligoWalkTool Content

http://rna.urmc.rochester.edu/servers/oligowalk

RNA > Structure Prediction, Visualization, and Design

OligoWalk is an online sever for designing efficient siRNA targeting a given mRNA sequence. By calculating thermodynamic features of sense-antisense hybidization, OligoWalk predicts the free energy changes of oligonucleotides binding to a target RNA.

NAR Web Server Issue 2008
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tagsmessenger rna nucleic acid hybridization oligonucleotides rna interference rna sequence analysis small interfering rna thermodynamics

psRNATargetTool Content

http://plantgrn.noble.org/psRNATarget/.

Model Organisms > Plants
RNA > Functional RNAs

psRNATarget is a plant small RNA target analysis server which features reverse complementary matching between small RNA and target transcript, and target site accessibility evaluation. It is designed for high-throughput analysis of next generation data, and outputs a comprehensive list of small RNA-target pairs.

NAR Web Server Issue 2011
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tagsmessenger rna micrornas plant gene expression regulation plant rna rna sequence analysis small interfering rna small untranslated rna

pssRNAMinerTool Content

http://bioinfo3.noble.org/pssRNAMiner/

Model Organisms > Plants
RNA > Functional RNAs

pssRNAMiner is a web server which identifies trans-acting siRNA clusters in plants, as well as their potential phase initiators. Users input a small RNA dataset and specify a transcript-genomic library for mapping.

NAR Web Server Issue 2008
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tagsgenomics micrornas plant gene expression regulation plant rna small interfering rna

SfoldTool Content

http://sfold.wadsworth.org

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

Server with three tools for the rational design of small interfering RNAs (Sirna), antisense oligonucleotides (Soligo), and trans-cleaving ribozymes (Sribo). A fourth tool, Srna, returns output including general folding features.

NAR Web Server Issue 2004
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tagsalgorithms animals antisense oligonucleotides antisense rna base sequence bayes theorem binding sites catalytic rna computational biology drug design escherichia coli molecular sequence data nucleic acid conformation phylogeny probability protozoan rna rabbits ribosomal rna rna rna stability small interfering rna spliced leader rna statistical distributions statistical models tetrahymena thermophila thermodynamics transfer rna xenopus laevis

siDirectTool Content

http://design.RNAi.jp/

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

Server for computing small interfering RNA (siRNA) sequences which are best suited for mammalian RNA interference (RNAi). The site accepts a sequence as input and returns a list of siRNA candidates.

NAR Web Server Issue 2004
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tagsalgorithms animals base sequence cell line chick embryo cricetinae drosophila gc rich sequence genetic models genetic vectors humans luciferases mammals mice molecular sequence data rna interference small interfering rna transfection

siRNA Selection ServerTool Content

http://jura.wi.mit.edu/bioc/siRNA

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

Server aiding the design of short interfering RNAs (siRNAs) by providing information on stability, SNPs and specificity of a potential siRNA.

This content is being maintained by lewitter.

NAR Web Server Issue 2004
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tagsalgorithms animals humans mice oligonucleotides rna interference small interfering rna

siVirusTool Content

http://sivirus.rnai.jp/

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

siVirus aids in the design of short interfering RNA (siRNA) and helps to identify conserved target sequences for antiviral RNA interference.

NAR Web Server Issue 2006
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tagsanti-hiv agents antiviral agents base sequence conserved sequence genetic variation rna interference rna viruses small interfering rna viral rna

TRODTool Content

http://www.cellbio.unige.ch/RNAi.html

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

T7 RNAi Oligo Designer (TROD) aids in the design of DNA oligonucleotides for short interfering RNA (siRNA) synthesis with T7 RNA polymerase. It takes an input of a cDNA sequence and outputs a list of DNA oligos for ordering.

NAR Web Server Issue 2004
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tagscell line dna-directed rna polymerases double-stranded rna gene silencing green fluorescent proteins hela cells humans luminescent proteins messenger rna molecular cloning molecular sequence data oligodeoxyribonucleotides plasmids recombinant fusion proteins rna interference small interfering rna transfection viral proteins