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Links tagged with 'rna interference'

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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

GenomeRNAiDatabase Content

http://rnai2.dkfz.de

Model Organisms > Databases

The GenomeRNAi database contains phenotypes from published cell-based RNA interference (RNAi) screens in Drosophila and Homo sapiens. The database connects observed phenotypes with annotations of targeted genes and information about the RNAi reagent used for the perturbation experiment. GenomeRNAi also enables reporting of data from microscopy experiments and curated phenotypes from published screens. In addition, the database provides an updated resource of RNAi reagents and their predicted quality that are available for the Drosophila and the human genome. GenomeRNAi also facilitates the integration with other genomic data sets and contains expression profiling (RNA-Seq) data for several cell lines commonly used in RNAi experiments.

NAR Database Issue 2010
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tagsanimals cell line computational biology drosophila melanogaster genetic databases genomics humans nucleic acid databases nucleic acid probes protein databases rna interference tertiary protein structure

miRTarBaseDatabase Content

http://miRTarBase.mbc.nctu.edu.tw/

RNA > Databases

miRTarBase database contains miRNA-target interactions (MTIs). The collected MTIs are validated experimentally by reporter assays, western blot, or microarray experiments with overexpression or knockdown of miRNAs.

NAR Database Issue 2011
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tagsgene expression regulation messenger rna micrornas nucleic acid databases reproducibility of results rna interference systems integration

MirZTool Content

http://www.mirz.unibas.ch

Expression > Gene Regulation
Expression > cDNA, EST, SAGE
RNA > Functional RNAs

MirZ is a web server that for evaluation and analysis of miRNA. It integrates two miRNA resources: the smiRNAdb miRNA expression atlas and the E1MMo miRNA target prediction algorithm.

NAR Web Server Issue 2009
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tagsalgorithms animals genomics humans messenger rna mice micrornas rats rna interference systems integration

MMIATool Content

http://cancer.informatics.indiana.edu/mmia

Expression > Gene Regulation
Expression > Transcript Expression Analysis
Human Genome > Genomics
RNA > Functional RNAs

microRNA and mRNA Integrated Analysis (MMIA) is a web server that integrates miRNA and mRNA expression data with predicted miRNA target information. MMIA incorporates miRNA prediction algorithms (TargetScan, PITA, PicTar).

NAR Web Server Issue 2009
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tagsgenetic databases humans messenger rna micrornas rna interference

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

RNAhybridTool Content

http://bibiserv.techfak.uni-bielefeld.de/rnahybrid/

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.

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

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

WormBaseDatabase Content

http://www.wormbase.org/

Model Organisms > Worm

Repository of mapping, sequencing and phenotypic information about C. elegans and C. briggsae.

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tagsanimals caenorhabditis caenorhabditis elegans data collection expressed sequence tags gene expression genomics helminth dna helminth rna neurons nucleic acid databases nucleic acid sequence homology rna interference single nucleotide polymorphism