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Links tagged with 'oligonucleotides'

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Found 14 links

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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

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

DSHIFTTool Content

http://www.chem.cuhk.edu.hk/DSHIFT/

DNA > Structure and Sequence Feature Detection

DSHIFT is a web server for predicting chemical shifts of DNA sequences in random coil form or double helical B-form.

NAR Web Server Issue 2007
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tagsalgorithms base sequence biomolecular nuclear magnetic resonance carbon computational biology computer simulation dna magnetic resonance spectroscopy molecular models molecular sequence data molecular structure nucleic acid conformation oligonucleotides phosphorus programming languages protons reproducibility of results sensitivity and specificity stochastic processes temperature

Gene2OligoTool Content

http://berry.engin.umich.edu/gene2oligo/

DNA > Tools For the Bench

Tool which divides both strands of an input DNA sequence into a set of contiguous oligonucleotides. These oligos are designed with complimentary regions so that the complete set can be combined to synthesize the input DNA sequence in vitro (using oligonucleotide synthesis and assembly PCR).

NAR Web Server Issue 2004
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tagsalgorithms cytochromes b5 dna ligases dna sequence analysis fungal genes nucleic acid hybridization oligonucleotides polymerase chain reaction saccharomyces cerevisiae temperature

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

oGNMTool Content

http://ignm.ccbb.pitt.edu/GNM_Online_Calculation.htm

Protein > Molecular Dynamics and Docking

Online Guassian Network Model (oGNM) calculates the equilibrium dynamics of any structure submitted in PDB format, using the Gaussian Network Model (GNM), a network model for representing biomolecules.

NAR Web Server Issue 2006
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tagsalgorithms binding sites chemical models computational biology computer simulation molecular models molecular structure motion normal distribution nucleic acid conformation oligonucleotides protein binding protein conformation protein databases protein folding protein sequence analysis proteins sequence alignment statistical models structure-activity relationship thermodynamics x-ray crystallography

OligoCalcTool Content

http://www.basic.northwestern.edu/biotools/OligoCalc.html

DNA > Tools For the Bench

OligoCalc calculates the physical properties of single- and double-stranded DNA and RNA molecules including melting temperature (multiple methods), concentration, molecular weight, and absorbance at 260 nanometers. OligoCalc can also account for 5’ and 3’ chemical modifications and predict potential hairpin loop formation.

NAR Web Server Issue 2007
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tagsalgorithms animals base composition chemical models computational biology dna humans oligonucleotides rna temperature

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

ProteinCCDTool Content

http://xtal.nki.nl/ccd

DNA > Tools For the Bench
Expression > Protein Expression
Protein > Domains and Motifs
Protein > Protein Expression
Protein > Sequence Data
Protein > Sequence Features
Protein > Sequence Retrieval

Protein Crystallographic Construct Design (Protein CCD) is a meta-web server that facilitates the design of several truncated constructs of a protein using experimental data or sequence analysis tools. From input DNA sequence, information on disorder, coiled coils, transmembrane segments, domains and domain linkers are collected from secondary structure prediction servers. Users can select starts and ends for protein constructs and ProteinCCD wil design suitable PCR primers.

NAR Web Server Issue 2009
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tagsamino acid sequence dna sequence analysis oligonucleotides polymerase chain reaction protein sequence analysis proteins secondary protein structure sequence deletion tertiary protein structure x-ray crystallography

QGRS MapperTool Content

http://bioinformatics.ramapo.edu/QGRS/index.php

DNA > Structure and Sequence Feature Detection
Expression > Splicing
RNA > Motifs
RNA > Structure Prediction, Visualization, and Design

Quadruplex forming G-Rich Sequences (QGRS) Mapper searches nucleotide sequences for the presence of G-quartet motifs. QGRS Mapper allows you to view the distribution and composition of QGRS in the context of alternatively spliced isoforms of your gene.

NAR Web Server Issue 2006
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tagsdna dna sequence analysis g-quadruplexes guanine oligonucleotides rna rna sequence analysis

Rescue-ESETool Content

http://genes.mit.edu/burgelab/rescue-ese/

DNA > Structure and Sequence Feature Detection
Expression > Splicing

Server for the identification of hexnucleotide exonic splicing enhancers (ESEs). Also contains a list of 238 identified ESEs for human genes.

NAR Web Server Issue 2004
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tagsanimals complementary dna computational biology consensus sequence dna sequence analysis exons genes human genome humans hypoxanthine phosphoribosyltransferase introns messenger rna mice nucleic acid databases nucleic acid regulatory sequences oligonucleotides point mutation ribonucleic acid regulatory sequences rna precursors rna sequence analysis rna splicing tetraodontiformes zebrafish

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

TmPrimeTool Content

http://prime.ibn.a-star.edu.sg

DNA > Mapping and Assembly
DNA > Tools For the Bench

TmPrime allows users to design oligonucleotide sets for gene assembly by both ligase chain reaction and polymerase chain reaction. The program also provides functions to separate long genes into smaller fragments for multi-pool assembly and codon optimization for expression.

NAR Web Server Issue 2009
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tagsdna sequence analysis humans ligase chain reaction oligonucleotides polymerase chain reaction proteins synthetic genes

Zinc Finger ToolsTool Content

http://www.scripps.edu/mb/barbas/zfdesign/zfdesignhome.php

DNA > Structure and Sequence Feature Detection
Expression > Gene Regulation

Zinc Finger Tools provides several tools for selecting zinc finger protein target sites and for designing the proteins that will target them.

NAR Web Server Issue 2006
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tagsamino acid sequence animals base sequence binding sites biomolecular nuclear magnetic resonance cell line combinatorial chemistry techniques computer simulation deoxyribonuclease i deoxyribonucleases dna dna primers dna sequence analysis dna-binding proteins down-regulation drug design enzyme-linked immunosorbent assay epidermal growth factor receptor erbb genes erbb-1 genes erbb-2 genes erbb-2 receptor erbb-3 receptor flow cytometry gene expression profiling gene expression regulation gene library gene targeting genetic promoter regions genetic transcription green fluorescent proteins histidine human genome humans kidney luminescent proteins lysine mice molecular cloning molecular models molecular sequence data mutation nucleic acid conformation oligonucleotides peptide library pliability polymerase chain reaction protein conformation protein engineering proteomics recombinant proteins reporter genes retroviridae secondary protein structure sequence analysis site-directed mutagenesis substrate specificity tertiary protein structure transcription factors transfection up-regulation x-ray crystallography zinc fingers