Oligo analysis tools
From MyBio
[edit] Categories which link here
[edit] Oligo analysis tools - Quick Links
| OligoCalc | ExonPrimer | |
| oligoTMcalc | Virtual PCR | |
| Oligo Calculator | Tm Determination | |
| Oligo Analyzer from Integrated DNA Technologies | Java Applet Oligonucleotide Analyzer |
[edit] Oligo analysis tools - Web Resources
OligoCalc
OligoCalc is a client-based (no data is submitted to the webserver) DNA and RNA oligonucleotide properties calculator that provides basic, salt-adjusted, and thermodynamic melting temperature calculations. It also provides calculations of the molecular weight, solution concentration, estimated absorbance coefficients, self-complementarity estimations and hairpin loop formation. The tool is open source.
ExonPrimer
ExonPrimer helps to design intron-specific primers for the PCR amplification of exons. The script needs a cDNA and the corresponding genomic sequence as input. It aligns these sequences using Blat and designs PCR primers to amplify each exon using Primer3
oligoTMcalc
Javascript oligo melt temperature calculator.
| DPL Forum: Too few categories! |
Virtual PCR
Carries out a virtual PCR reaction simulation and displays picture of predicted agarose gel. VPCR 2.0 searches the specified database for matches to the primers. If matches are found within 10000 bases, a PCR simulation model predicts amplification. Calculated PCR products are displayed within a minute.
Oligo Calculator
Calculates the melting temperature of an oligonucleotide.
Tm Determination
Tm calculations as described by Breslauer PNAS 83 p3746.
Oligo Analyzer from Integrated DNA Technologies
Calculates melting temperature and molecular weightpredicts Hairpin structuresself and hetero dimerizationincludes Blast search and calculates Tm for single base mismatch primer.
Java Applet Oligonucleotide Analyzer
Free Java applet to calculate properties of PCR primers. Generates Tm, free energy, molecular weight and hairpin and dimer formation structures.
