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Links tagged with 'nucleic acid denaturation'

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Found 10 links

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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

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

MfoldTool Content

http://mfold.rna.albany.edu/?q=mfold/download-mfold

RNA > Structure Prediction, Visualization, and Design

Predict RNA secondary structure from sequence; does not predict pseudoknots - see PKNOTS.

NAR Web Server Issue 2003
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tagsbase composition base sequence consensus sequence dna molecular models molecular sequence data nucleic acid conformation nucleic acid databases nucleic acid denaturation nucleic acid hybridization nucleic acid repetitive sequences rna single-stranded dna thermodynamics

NNDBDatabase Content

http://rna.urmc.rochester.edu/NNDB

DNA > Databases

The Nearest Neighbor Database (NNDB) is a web-based resource for disseminating parameter sets for predicting nucleic acid secondary structure stabilities. For each set of parameters, the database includes the set of rules with descriptive text, sequence-dependent parameters in plain text and html, literature references to experiments and usage tutorials. Also covered are parameters for predicting RNA folding free energy and enthalpy changes.

NAR Database Issue 2010
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tagsalgorithms base sequence computational biology genetic databases molecular sequence data nucleic acid conformation nucleic acid databases nucleic acid denaturation rna thermodynamics

OligoHeatMapTool Content

http://bioinfo.unice.fr/ohm/

DNA > Tools For the Bench

OligoHeatMap is an online tool for estimation of melting temperatures for sets of oligonucleotides and positioning of oligomers within sets of aligned sequences. Oligomer positioning on sequences is displayed graphically.

NAR Web Server Issue 2008
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tagsdna sequence analysis nucleic acid denaturation nucleic acid hybridization oligonucleotide probes polymerase chain reaction sequence alignment thermodynamics

OligoWizTool Content

http://www.cbs.dtu.dk/services/OligoWiz2/

DNA > Tools For the Bench
Expression > Transcript Expression Analysis

OligoWiz 2.0 is a client for microarray probe design that allows for the integration of sequence annotations, probe quality parameters, and the placement of multiple probes per transcript.

NAR Web Server Issue 2005NAR Web Server Issue 2003
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tagsalgorithms dna primers gene expression profiling genetic transcription molecular sequence data nucleic acid conformation nucleic acid denaturation oligonucleotide array sequence analysis oligonucleotide probes reproducibility of results rna sequence analysis saccharomyces cerevisiae systems integration temperature

PDATool Content

http://dbb.nhri.org.tw/primer/

DNA > Tools For the Bench

Primer Design Assistant (PDA) is a PCR primer design tool that will accept batch submissions of query sequences.

NAR Web Server Issue 2003
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tagsdimerization dna primers dna sequence analysis gc rich sequence nucleic acid conformation nucleic acid denaturation polymerase chain reaction thermodynamics

Stitchprofiles.uio.noTool Content

http://stitchprofiles.uio.no/

DNA > Tools For the Bench

Stitchprofiles.uio.no is a server that performs web-based computations on DNA melting. In addition to creating stitch profile diagrams representing the alternative conformations that partly melted DNA can adopt, the server can also plot the classical melting curves, probability profiles, and temperature profiles.

NAR Web Server Issue 2005
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tagsalgorithms base sequence dna dna sequence analysis nucleic acid conformation nucleic acid denaturation statistical models temperature thermodynamics

TGGE-STARTool Content

http://www.charite.de/bioinf/tgge/

DNA > Tools For the Bench

TGGE-STAR assists in the design of PCR primers for temperature gradient gel electrophoresis. It also incorporates the concept of bipolar clamping.

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tagsdna primers humans microfilament proteins mutation nucleic acid denaturation polyacrylamide gel electrophoresis temperature

WEB-THERMODYNTool Content

http://www.gsa.buffalo.edu/dna/dk/WEBTHERMODYN/

DNA > Structure and Sequence Feature Detection

WEB-THERMODYN analyzes DNA sequences and computes the DNA helical stability. This tool can be used to predict sites of low helical stability present at regulatory regions for transcription and replication.

NAR Web Server Issue 2003
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tagsdeoxyribonucleases dna dna replication dna sequence analysis fungal chromosomes fungal dna mutation nucleic acid conformation nucleic acid denaturation nucleic acid regulatory sequences plasmids replication origin replicon saccharomyces cerevisiae thermodynamics