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Links tagged with 'dna primers'

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Found 34 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

Defining Transcriptional Programs in Vascular EndotheliumResource Content

http://www.vessels.bwh.harvard.edu/

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.

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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

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

DNannotatorTool Content

http://bioapp.psych.uic.edu/DNannotator.htm

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.

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/

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.

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/

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.

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

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.

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

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.

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/

DNA > Tools For the Bench

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

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tagsalgorithms dna primers dna sequence analysis polymerase chain reaction

IccareTool Content

http://genopole.toulouse.inra.fr/bioinfo/Iccare/

Sequence Comparison > Other Alignment Tools

The Iccare (Interspecific Comparative Clustering and Annotation foR Est) web server compares all available EST and mRNA sequences for a query organism against the set of transcripts for a reference organism. The results are presented graphically and relative to the location of genes on the chromosomes of the reference organism.

NAR Web Server Issue 2004
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tagsanimals arabidopsis chromosome mapping dna primers dna sequence analysis expressed sequence tags human genome humans messenger rna nucleic acid databases nucleic acid probes nucleic acid sequence homology plant genes rna sequence analysis rna splice sites systems integration

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

MADAPTool Content

http://ccg.vital-it.ch/madap/

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).

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

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.

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/

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.

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/

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