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Links tagged with 'temperature'

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Found 13 links

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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

DisEMBLTool Content

http://dis.embl.de/

Protein > 2-D Structure Prediction
Protein > 3-D Structure Prediction

A computational tool for prediction of disordered/unstructured regions within a protein sequence.

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tagscircular dichroism humans ligands magnetic resonance spectroscopy neural networks (computer) protein conformation proteins proteome sensitivity and specificity src homology domains statistics as topic temperature theoretical models ultraviolet rays x-ray crystallography

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

eProbalignTool Content

http://probalign.njit.edu/probalign/login

Sequence Comparison > Analysis of Aligned Sequences
Sequence Comparison > Multiple Sequence Alignments

eProbalign computes maximal expected accuracy multiple sequence alignments from partition function posterior probabilities. eProbalign also provides a platform to visualize the alignment, generate images, and manipulate the output.

NAR Web Server Issue 2007
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tagsalgorithms amino acid sequence amino acid sequence homology animals computational biology computer simulation dna genetic databases humans molecular sequence data probability protein sequence analysis sequence alignment software design statistical models temperature thermodynamics

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

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

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

PrimerStationTool Content

http://ps.cb.k.u-tokyo.ac.jp/

DNA > Tools For the Bench
Human Genome > Other Resources

PrimerStation is a multiplex genomic PCR primer design tool specific for the human genome.

NAR Web Server Issue 2006
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tagsdna primers genomics human genome humans polymerase chain reaction temperature

RosettaDesignTool Content

http://rosettadesign.med.unc.edu

Protein > 3-D Structure Prediction
Protein > Biochemical Features

RosettaDesign identifies low energy sequences for specified protein three dimensional (3D) structures and can been used to predict stable side chain conformations.

NAR Web Server Issue 2006
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tagsalgorithms amino acid sequence amino acid sequence homology bacterial proteins biomolecular nuclear magnetic resonance circular dichroism computational biology computer simulation crystallization dimerization dna-binding proteins guanidine kinetics magnetic resonance spectroscopy molecular models molecular sequence data monte carlo method mutagenesis mutation protein conformation protein databases protein denaturation protein engineering protein folding protein sequence analysis proteins secondary protein structure sequence alignment solubility temperature tertiary protein structure thermodynamics x-ray crystallography

SrideTool Content

http://sride.enzim.hu/

Protein > 3-D Structural Features

Sride is a tool for identificating stabilizing residues in protein structure.

NAR Web Server Issue 2005
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tagsamino acids conserved sequence hydrophobic and hydrophilic interactions molecular evolution molecular models pliability protein conformation protein folding proteins secondary protein structure temperature tertiary protein structure thermodynamics

SSEPTool Content

http://cluster.physics.iisc.ernet.in/ssep/options.html

Protein > 2-D Structure Prediction

Secondary Structural Elements of Proteins (SSEP) provides access to information about secondary structural elements present in non-redundant sets of proteins from the PDB.

NAR Web Server Issue 2003
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tagsartificial intelligence computational biology molecular models protein databases proteins secondary protein structure temperature x-ray crystallography

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