> Tag > Links tagged with 'nucleic acid hybridization'

Links tagged with 'nucleic acid hybridization'

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AsteriasTool Content

http://asterias.bioinfo.cnio.es/ [open in a new window]

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DNA > Annotations
Expression > Transcript Expression Analysis

Asterias is a set of tools for the analyses of high throughput genomic data that includes applications for microarray data normalization, filtering, detection of differential gene expression, class and survival prediction model building, and analysis of array CGH data. Most applications use parallel computing resulting in significant increases in speed.

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links directory index: 555
TitlePublication YearGoogle Scholar Citation Count
Asterias: integrated analysis of expression and aCGH data using an open-source, web-based, parallelized software suite200713
Gene selection and classification of microarray data using random forest2006485
DNMAD: web-based diagnosis and normalization for microarray data200457
NAR Web Server Issue 2007
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tagsalgorithms animals automated pattern recognition automation cluster analysis computational biology computer simulation database management systems dna sequence analysis gene expression profiling genetic models genomics humans nucleic acid hybridization oligonucleotide array sequence analysis programming languages sequence alignment statistical models

Defining Transcriptional Programs in Vascular EndotheliumResource Content

http://www.vessels.bwh.harvard.edu/ [open in a new window]

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Expression > Gene Regulation
Expression > Transcript Expression Analysis

This website contains microarray analysis software (Argus and Z-pool), an Endothelial Cell Expression Database, and other resources related to Vascular Endothelium research. See the PubMed abstracts for more information.

links directory index: 398
TitlePublication YearGoogle Scholar Citation Count
Improving the statistical detection of regulated genes from microarray data using intensity-based variance estimation200426
Biomechanical activation of vascular endothelium as a determinant of its functional phenotype2001355
Argus--a new database system for Web-based analysis of multiple microarray data sets200117
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tagsbase sequence biomechanics complementary dna cultured cells dna primers factual databases gene expression profiling humans molecular sequence data nucleic acid hybridization oligonucleotide array sequence analysis phenotype reproducibility of results statistics as topic vascular endothelium

DINAMeltTool Content

http://mfold.rna.albany.edu/?q=DINAMelt [open in a new window]

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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.

links directory index: 944
TitlePublication YearGoogle Scholar Citation Count
DINAMelt web server for nucleic acid melting prediction2005378
Prediction of hybridization and melting for double-stranded nucleic acids2004129
Coaxial stacking of helixes enhances binding of oligoribonucleotides and improves predictions of RNA folding1994437
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

dnaMATETool Content

http://protein.bio.puc.cl/cardex/servers/dnaMATE/index.html [open in a new window]

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DNA > Tools For the Bench

dnaMATE calculates a consensus melting temperature (Tm) for any given short DNA sequence (16-30 nts) based on three independent thermodynamic data tables. Stand-alone version available; list of other melting temperature calculation servers also provided.

links directory index: 77
TitlePublication YearGoogle Scholar Citation Count
dnaMATE: a consensus melting temperature prediction server for short DNA sequences200519
Comparison of different melting temperature calculation methods for short DNA sequences200558
NAR Web Server Issue 2005
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tagsalgorithms benchmarking chemical models computer simulation dna dna sequence analysis nucleic acid denaturation nucleic acid hybridization oligonucleotides temperature transition temperature

MatchMinerTool Content

http://discover.nci.nih.gov/matchminer/ [open in a new window]

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Expression > Transcript Expression Analysis

MatchMiner is a tool to compare and convert gene identifiers. Users can translate single or lists of identifiers from one form to another, or compare two lists of identifiers for common gene references.

links directory index: 150
TitlePublication YearGoogle Scholar Citation Count
MatchMiner: a tool for batch navigation among gene and gene product identifiers2003150
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tagsalgorithms computational biology dna sequence analysis fluorescence in situ hybridization genetic databases genomics humans nucleic acid hybridization oligonucleotide array sequence analysis proteins rna software design

OligoHeatMapTool Content

http://bioinfo.unice.fr/ohm/ [open in a new window]

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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.

links directory index: 14
TitlePublication YearGoogle Scholar Citation Count
OligoHeatMap (OHM): an online tool to estimate and display hybridizations of oligonucleotides onto DNA sequences200814
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

OligoWalkTool Content

http://rna.urmc.rochester.edu/servers/oligowalk [open in a new window]

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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.

links directory index: 14
TitlePublication YearGoogle Scholar Citation Count
OligoWalk: an online siRNA design tool utilizing hybridization thermodynamics200814
NAR Web Server Issue 2008
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tagsmessenger rna nucleic acid hybridization oligonucleotides rna interference rna sequence analysis small interfering rna thermodynamics

PLANdbAffyDatabase Content

http://affymetrix2.bioinf.fbb.msu.ru [open in a new window]

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Expression > Databases

PLANdbAffy contains the results of the alignment of probe sequences from five Affymetrix expression microarrays to the human genome. Probes matching the transcript-coding regions in the correct orientation have been determined. For each such probe alignment region, the mRNA and EST sequences that contain the probe sequence have also been determined. In the textual part of the database interface, data on the sequences that cover the probe alignment region and SNPs that are located inside it is summarized. The graphical part of our database interface is implemented as custom tracks to the UCSC genome browser that allows one to utilize all the data that are offered by UCSC browser.

links directory index: 6
TitlePublication YearGoogle Scholar Citation Count
PLANdbAffy: probe-level annotation database for Affymetrix expression microarrays20106
NAR Database Issue 2010
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tagsalternative splicing computational biology genetic databases genome humans introns nucleic acid databases nucleic acid hybridization oligonucleotide array sequence analysis protein databases sequence alignment single nucleotide polymorphism

TIARADatabase Content

http://tiara.gmi.ac.kr [open in a new window]

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DNA > Databases
Human Genome > Databases

Total Integrated Archive of Short-Read and Array (TIARA) database, contains personal genomic information obtained from next generation sequencing (NGS) techniques and ultra-high-resolution comparative genomic hybridization (CGH) arrays. This database improves the accuracy of detecting personal genomic variations, such as SNPs, short indels and structural variants (SVs).

links directory index: 4
TitlePublication YearGoogle Scholar Citation Count
TIARA: a database for accurate analysis of multiple personal genomes based on cross-technology20114
NAR Database Issue 2011
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tagsdna sequence analysis genetic variation genomics high-throughput nucleotide sequencing human genome humans nucleic acid databases nucleic acid hybridization

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