> Tag > Links tagged with 'dna primers'

Links tagged with 'dna primers'

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Found 26 links

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DePIETool Content

http://biocore.unl.edu/primer/primerPI.html [open in a new window]

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DNA > Tools For the Bench
Protein > Networks & Interactions, Pathways and Enzymes

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

links directory index: 4
TitlePublication YearGoogle Scholar Citation Count
DePIE: Designing Primers for Protein Interaction Experiments20034
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

DNannotatorTool Content

http://bioapp.psych.uic.edu/DNannotator.htm [open in a new window]

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DNA > Annotations
Human Genome > Annotations

DNannotator is a tool that performs de novo annotation of SNPs, STSs, and exons. It also allows for the migration of user-defined annotations onto different versions of genomic sequences (<30Kb size limit).

This content is being maintained by cliu.

links directory index: 14
TitlePublication YearGoogle Scholar Citation Count
Frequency Finder: a multi-source web application for collection of public allele frequencies of SNP markers20047
DNannotator: Annotation software tool kit for regional genomic sequences20037
NAR Web Server Issue 2003
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tagsalgorithms dna primers dna sequence analysis gene frequency genetic databases genetic markers genomics human chromosomes human genome humans sequence alignment sequence tagged sites single nucleotide polymorphism

DyNAVacSTool Content

http://miracle.igib.res.in/dynavac/ [open in a new window]

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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.

links directory index: 11
TitlePublication YearGoogle Scholar Citation Count
DyNAVacS: an integrative tool for optimized DNA vaccine design200611
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/ [open in a new window]

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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.

links directory index: 579
TitlePublication YearGoogle Scholar Citation Count
E-RNAi: a web application for the multi-species design of RNAi reagents--2010 update20104
E-RNAi: a web application to design optimized RNAi constructs200565
Genome-wide RNAi analysis of growth and viability in Drosophila cells2004510
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

Electronic PCRDatabase Content

http://www.ncbi.nlm.nih.gov/sutils/e-pcr [open in a new window]

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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.

links directory index: 242
TitlePublication YearGoogle Scholar Citation Count
A web server for performing electronic PCR200418
Sequence mapping by electronic PCR1997224
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

GeMprospectorTool Content

http://cgi-www.daimi.au.dk/cgi-chili/GeMprospector/main [open in a new window]

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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.

links directory index: 19
TitlePublication YearGoogle Scholar Citation Count
GeMprospector--online design of cross-species genetic marker candidates in legumes and grasses200619
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

GenefisherTool Content

http://bibiserv.techfak.uni-bielefeld.de/genefisher/ [open in a new window]

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DNA > Tools For the Bench

Interactive primer design tool for standard or degenerate primers; will accept unaligned sequences.

links directory index: 121
TitlePublication YearGoogle Scholar Citation Count
GeneFisher--software support for the detection of postulated genes1996121
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tagsalgorithms dna primers dna sequence analysis polymerase chain reaction

IDT SciToolsTool Content

http://www.idtdna.com/SciTools/SciTools.aspx [open in a new window]

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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.

links directory index: 22
TitlePublication YearGoogle Scholar Citation Count
IDT SciTools: a suite for analysis and design of nucleic acid oligomers200822
NAR Web Server Issue 2008
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tagsantisense oligonucleotides dna primers nucleic acid conformation oligonucleotide probes oligonucleotides small interfering rna

Institute of Enzymology ServersTool Content

http://www.enzim.hu/index.php?option=com_content&task=blogcategory&id=30&Itemid=... [open in a new window]

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Protein > 2-D Structure Prediction
Protein > 3-D Structure Prediction
Protein > Localization and Targeting

A set of severs developed by the Institute of Enzymology that includes tools for transmembrane protein structure prediction and structural analyses.

links directory index: 2004
TitlePublication YearGoogle Scholar Citation Count
TMDET: web server for detecting transmembrane regions of proteins by using their 3D coordinates200546
IUPred: web server for the prediction of intrinsically unstructured regions of proteins based on estimated energy content2005392
The pairwise energy content estimated from amino acid composition discriminates between folded and intrinsically unstructured proteins2005235
BiSearch: primer-design and search tool for PCR on bisulfite-treated genomes200552
PDB_TM: selection and membrane localization of transmembrane proteins in the protein data bank2005138
Transmembrane proteins in the Protein Data Bank: identification and classification2004138
Locating the stabilizing residues in (alpha/beta)8 barrel proteins based on hydrophobicity, long-range interactions, and sequence conservation200443
SCide: identification of stabilization centers in proteins.20030
Servers for sequence-structure relationship analysis and prediction20035
On filtering false positive transmembrane protein predictions200257
The HMMTOP transmembrane topology prediction server.20010
Principles governing amino acid composition of integral membrane proteins: application to topology prediction1998795
Stabilization centers in proteins: identification, characterization and predictions1997103
NAR Web Server Issue 2003
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tagsalgorithms amino acid sequence amino acids binding sites capsid proteins cell line chemical models computational biology computer simulation conserved sequence cysteine database management systems dna methylation dna primers drug stability energy transfer genome genomics humans hydrophobic and hydrophilic interactions kringles lipid bilayers markov chains membrane proteins molecular models molecular sequence data neural networks (computer) oxidation-reduction pliability polymerase chain reaction protein binding protein conformation protein databases protein engineering protein folding protein sequence analysis proteins reproducibility of results secondary protein structure sequence alignment statistical models structure-activity relationship sulfites temperature tertiary protein structure thermodynamics tissue plasminogen activator

MADAPTool Content

http://ccg.vital-it.ch/madap/ [open in a new window]

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DNA > Annotations
Expression > Gene Regulation
Human Genome > Annotations

MADAP is a clustering tool for the interpretation annotation data mapped onto complete or partial genome sequences. Initially developed for determining transcription start sites (TSS) by defining 5\' and 3\'ends of mRNA, MADAP also has utility in clustering other annotation data types (ChIP-chip data, for example).

links directory index: 90
TitlePublication YearGoogle Scholar Citation Count
MADAP, a flexible clustering tool for the interpretation of one-dimensional genome annotation data20075
The Eukaryotic Promoter Database EPD: the impact of in silico primer extension200485
NAR Web Server Issue 2007
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tagsalgorithms animals base sequence chromatin immunoprecipitation cluster analysis complementary dna computational biology dna primers eukaryotic cells expressed sequence tags genetic databases genetic promoter regions genome humans nucleic acid databases open reading frames response elements statistical models

MutScreenerTool Content

http://bioinfo.bsd.uchicago.edu/MutScreener.html [open in a new window]

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DNA > Tools For the Bench

MutScreener is a human-specific primer design tool that considers gene annotation information to design primers for mutation screening. Users can provide custom gene annotation or use existing public gene annotations.

links directory index: 7
TitlePublication YearGoogle Scholar Citation Count
MutScreener: primer design tool for PCR-direct sequencing20067
NAR Web Server Issue 2006
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tagsdna primers exons genetic promoter regions genomics human genome humans polymerase chain reaction

NTMGTool Content

http://oblab.cs.nchu.edu.tw:8080/WebSDL/ [open in a new window]

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DNA > Tools For the Bench

NTMG (N-Terminal Truncated Mutants Generator) is a tool for generating multiplex PCR primers for designing N-terminal truncated mutants.

links directory index: 1
TitlePublication YearGoogle Scholar Citation Count
NTMG (N-terminal Truncated Mutants Generator for cDNA): an automatic multiplex PCR assays design for generating various N-terminal truncated cDNA mutants20071
NAR Web Server Issue 2007
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tagsalgorithms automation complementary dna dna primers dna sequence analysis gene deletion humans mutagenesis mutation polymerase chain reaction single nucleotide polymorphism

OligoWizTool Content

http://www.cbs.dtu.dk/services/OligoWiz2/ [open in a new window]

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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.

links directory index: 175
TitlePublication YearGoogle Scholar Citation Count
OligoWiz 2.0--integrating sequence feature annotation into the design of microarray probes200565
Design of oligonucleotides for microarrays and perspectives for design of multi-transcriptome arrays2003110
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/ [open in a new window]

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DNA > Tools For the Bench

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

links directory index: 53
TitlePublication YearGoogle Scholar Citation Count
Primer Design Assistant (PDA): A web-based primer design tool200353
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

PHUSERTool Content

http://www.cbs.dtu.dk/services/phuser/ [open in a new window]

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DNA > Tools For the Bench

Primer Help for Uracil Specific Exision Reagent (PHUSER) is a tool for designing primers specifically for USER fusion and USER cloning applications. Standard primer analyses are also conducted.

links directory index: 2
TitlePublication YearGoogle Scholar Citation Count
PHUSER (Primer Help for USER): a novel tool for USER fusion primer design20112
NAR Web Server Issue 2011
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tagsdna dna primers molecular cloning polymerase chain reaction uracil

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