> > Tools For the Bench

Tools For the Bench

These links contain programs which can create restriction enzyme maps for your sequence of interest. Also included are tools for the design of oligonucleotide probes and PCR primers.

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Found 63 links

Displaying 15 links

ASePCRTool Content

http://genome.ewha.ac.kr/ASePCR/

DNA > Tools For the Bench
Expression > Splicing

ASePCR (Alternative Splicing electronic PCR) is a tool for carrying out e-PCR to detect differences in amplicon sizes in transcripts from different tissues and organs.

NAR Web Server Issue 2005
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tagsalgorithms alternative splicing animals base sequence expressed sequence tags humans messenger rna mice molecular sequence data rats reverse transcriptase polymerase chain reaction tissue distribution

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

Bioinformatics ToolkitTool Content

http://toolkit.tuebingen.mpg.de/

DNA > Annotations
DNA > DNA and Genomic Analysis
DNA > Phylogeny Reconstruction
DNA > Structure and Sequence Feature Detection
DNA > Tools For the Bench
Human Genome > Annotations
Protein > 2-D Structure Prediction
Protein > 3-D Structure Prediction
Protein > Do-it-all Tools for Protein
Protein > Localization and Targeting
Protein > Molecular Dynamics and Docking
Protein > Phylogeny Reconstruction
Protein > Sequence Comparison
Protein > Sequence Features
Sequence Comparison > Multiple Sequence Alignments

This Toolkit is a collection of a wide range of tools and links for sequence analysis, function, and structure prediction. This resource offers convienent web interfaces for many freely available tools.

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chipDTool Content

http://chipd.uwbacter.org

DNA > Tools For the Bench

chipD is a web server that facilitates the design of DNA oligonucleotide probes for high-density tiling arrays. The algorithm ensures probe specificity, thermodynamic properties amongst probe sets and target sequence coverage.

This content is being maintained by ydufour.

NAR Web Server Issue 2010
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tagsalgorithms gene expression profiling oligonucleotide array sequence analysis oligonucleotide probes rhodobacter sphaeroides

CODEHOPTool Content

http://blocks.fhcrc.org/codehop.html

DNA > Tools For the Bench

COnsensus-DEgenerate Hybrid Oligonucleotide Primers (CODEHOP); degenerate PCR primer design; will accept unaligned sequences.

NAR Web Server Issue 2003
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tagsamino acid sequence base sequence consensus sequence dna primers oligonucleotides polymerase chain reaction protein sequence analysis sequence alignment

DePIETool Content

http://biocore.unl.edu/primer/primerPI.html

DNA > Tools For the Bench
Protein > Interactions, Pathways, Enzymes

Design Primers for Protein Interaction Experiments (DePIE) is a web-based primer design tool for protein interaction experiments.

NAR Web Server Issue 2003
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tagsdna primers nucleic acid databases nucleic acid denaturation polymerase chain reaction protein databases protein sorting signals proteins sequence analysis tertiary protein structure two-hybrid system techniques yeasts

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

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

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

DyNAVacSTool Content

http://miracle.igib.res.in/dynavac/

DNA > Tools For the Bench
Human Genome > Health and Disease

DyNAVacS is a tool for designing DNA vaccines that includes steps for chosing a suitable expression vector, ensuring optimal expression by codon optimization, engineering CpG motifs for enhancing immune responses, and providing additional sequence signals for efficient translation. It also allows includes restriction enzyme mapping and design of primers spanning user specified sequences.

NAR Web Server Issue 2006
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tagscodon computational biology cpg islands dna primers dna vaccines drug design gene expression polymerase chain reaction restriction mapping systems integration

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

eBioinformaticsResource Content

http://www.ebioinformatics.org/

DNA > DNA and Genomic Analysis
DNA > Mapping and Assembly
DNA > Structure and Sequence Feature Detection
DNA > Tools For the Bench
Protein > Biochemical Features
Protein > Do-it-all Tools for Protein
Protein > Presentation and Format
Protein > Sequence Features
Sequence Comparison > Multiple Sequence Alignments
Sequence Comparison > Pairwise Sequence Alignments
Sequence Comparison > Similarity Searching

This site provides several bioinformatics software tools packaged together for easy installation on MacOSX computers. The software includes NCBI tools, EMBOSS, ClustalW, Staden, T-Coffee and Primer3.

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Electronic PCRDatabase Content

http://www.ncbi.nlm.nih.gov/sutils/e-pcr

DNA > Tools For the Bench

Find sequence-based markers (STSs) and therefore, map location in a DNA sequence of interest; useful for detecting mis-priming events.

NAR Web Server Issue 2004
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tagsalgorithms base sequence chromosome mapping computational biology dna primers dna sequence analysis factual databases human chromosomes humans molecular sequence data nucleic acid databases polymerase chain reaction sequence alignment sequence tagged sites

EMBOSSTool Content

http://emboss.bioinformatics.nl/

DNA > DNA and Genomic Analysis
DNA > Sequence Retrieval and Submission
DNA > Structure and Sequence Feature Detection
DNA > Tools For the Bench
Protein > Biochemical Features
Protein > Do-it-all Tools for Protein
Protein > Presentation and Format
Protein > Sequence Features
Protein > Sequence Retrieval
RNA > Sequence Retrieval
Sequence Comparison > Alignment Editing and Visualization
Sequence Comparison > Multiple Sequence Alignments
Sequence Comparison > Pairwise Sequence Alignments
Sequence Comparison > Similarity Searching

Diverse suite of tools for sequence analysis; many programs analagous to GCG; context-sensitive help for each tool.

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tagsmolecular biology sequence alignment

GeMprospectorTool Content

http://cgi-www.daimi.au.dk/cgi-chili/GeMprospector/main

DNA > Tools For the Bench
Expression > cDNA, EST, SAGE
Model Organisms > Plants

GeMprospector is designed to find cross-species genetic marker candidates in legumes and grasses. GeMprospector automates PCR primer design based on multiple sequence alignments of submitted ESTs and their homologues in sequence databases from legumes or grasses.

NAR Web Server Issue 2006
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tagsbase sequence conserved sequence dna primers expressed sequence tags fabaceae genetic markers genetic polymorphism genomics nucleic acid databases poaceae polymerase chain reaction sequence alignment

Tags associated with subcategory 'DNA/Tools For the Bench'

polymerase chain reaction dna primers algorithms dna sequence analysis humans base sequence animals sequence alignment genomics molecular sequence data nucleic acid denaturation small interfering rna oligonucleotides nucleic acid databases computational biology temperature dna cattle gene expression profiling complementary dna dna probes polyacrylamide gel electrophoresis chickens nucleic acid hybridization oligonucleotide probes bayes theorem binding sites catalytic rna antisense rna antisense oligonucleotides dna ligases fungal genes saccharomyces cerevisiae single nucleotide polymorphism rna sequence analysis mutation essential genes gene knockdown techniques genome genomic library drosophila proteins drosophila melanogaster nucleic acid repetitive sequences genotype core binding factor alpha 2 subunit dna-binding proteins cultured cells indicators and reagents inhibitor of apoptosis proteins systems integration morpholines synthetic genes microfilament proteins reproducibility of results transcription factors insect genes phenotype proteome sequence homology proto-oncogene proteins probability drug design viral proteins rna stability spliced leader rna statistical distributions transfection rna interference single-stranded dna structure-activity relationship theoretical models transition temperature chromosome mapping genetic transcription restriction mapping substrate specificity type ii site-specific deoxyribonucleases nucleic acid sequence homology plasmids xenopus laevis oligonucleotide array sequence analysis statistical models tetrahymena thermophila transfer rna thermodynamics recombinant fusion proteins oligodeoxyribonucleotides cell line chick embryo cricetinae drosophila rna ribosomal rna escherichia coli nucleic acid conformation phylogeny rabbits protozoan rna gc rich sequence genetic models hela cells