Useful links and downloads

Web tools

Sequence selection tools

BLAST
Tool for sequence search in databases

ClustalW
Multiple sequence alignment program for DNA or proteins

Ensembl
Database with several annotated eukaryotic genomes

GeneCards human gene database
Database of known and predicted human genes and gene related information

Ingenuity
Gene database from Sigma

mirSearch
Quickly find microRNAs involved in your area of research

NCBI
Database with all available DNA sequences

SpliceMiner
Tool to look for known splice variants

UCSC Genome Bioinformatics
Information of genes from different databases in one place. Provides very fast In-Silico PCR tool.


Pre-designed primers and probes databases

Primer bank
Database of predesigned qPCR primers and probes

Real-time PCR primer and probe sets
Database of predesigned qPCR primers and probes

RTPrimerDB- primer and probe database
Database of predesigned qPCR primers and probes


Primer design tools

Exon Primer
Tool for designing exon-spanning primers

Primer3
Tool for web-based primer design

Primer-BLAST
Finding primers specific to your PCR template (using Primer3 and BLAST)

RealTimeDesign
Tool for web-based qPCR primer design


Tools for evaluating designed PCR systems

Beacon Designer Free Edit
Online tool for analyzing SYBR® Green primers and TaqMan® probes

mFold
Tool for checking secondary structures of DNA or RNA

Netprimer
Tool for analyzing primers for Tm, secondary structures and primerdimer formation


Tools for evaluating oligonucleotide properties

Copy number calculator
Tool for calculating the number of copies of a template

DNA melt-point calculator
Tool for calculating the melting temperatures of oligonucleotides

DNA/RNA Absorption Concentration Calculator
Tool for converting measured absorption to concentration of DNA or RNA in your sample

Oligonucleotide Properties Calculator
Tool for establishing the physical and chemical properties of oligonucleotides

Poland
Determine Tm for your amplicon before running a HRM assay.


Tools for Digital PCR

uCount
Calculator for the mean and confidence intervals for digital PCR data.


BioMarkers

The Global Alliance for Genomics and Health
An international coalition, formed to enable the sharing of genomic and clinical data

The International Cancer Genome Consortium

The Cancer Genome Atlas


 

Protocols and links

Gene Quantification web page
Describes and summarizes technical aspects in gene quantification using qPCR

Genome Technology Tech Guide

qPCR net
News about qPCR related events, companies and products

The MIQE guidelines
Minimum Information for Publication of Quantitative Real-Time PCR Experiments

MIQE_Checklist


Forums and newsgroups

Biotechniques Molecular Biology Discussion forum

GenEx discussion forum


Downloads

Beacon Designer and Allelle ID
Download free trial version of Beacon Designer and Allelle ID

GenEx
Download the 14-day-free evaluation copy of GenEx Data Analysis Software