DNA Resources

IDT Biophysics

• IDT is useful for calculating the extinction coefficient across the the entire UV spectrum of a typical oligonucleotide sequence (215 - 310 nm). It also has a useful Tm (UV melting) prediction tool, which also factors in salt concentration as well as mismatches and deletions within the sequence.
  UV Spectrum Tool
  Tm Prediction Tool
  

  
  
  

RiboTask

• RiboTask can perform extinction coefficient and mass calculations, and is useful as it can do this for other forms of sequences (RNA, UNA, LNA) and includes a comprehensive list of modifications, labels and spacers.
  RiboTask calculator
  

  
  
  

Mongo Oligo Calculator

• Mongo oligo mass calculator is useful for the analysis of oligonucleotide mass spec data. It can calculate the predicted mass of a sequence as well as calculating internal fragmentation, base loss and electrospray series peaks. It can perform this on both DNA and RNA.
  Mongo Oligo Mass Calculator
  

  
  
  

Northwestern Oligo Calc

• Northwestern oligo calc can perform a range of functions similar to the resources listed above, but can also determine some additional thermodynamic properties.
  Northwestern Oligo Calc
  

  
  
  

Calc Tool

• CalcTool is useful for calculating the distances of oligonucleotide sequences, given the number of base pairs in a number of scientific units, it will also give you the number of helical turns for the sequence.
  Calc Tool
  

  
  
  

Blast

• BLAST is a tool that can find similarities between biological sequences in a range of genomes. This can be done on both DNA and protein sequences.
  Blast
  

  
  
  

PFG Buffer Calc

• PFG Buffer Calc is a very useful tool in calculating the quantities of reagents needed to produce buffers needed for the analysis of oligonucleotide sequences. It will also provide the recipe and instructions to produce the required buffer.
  BFG Buffer Calc
  

  
  
  

Mass Spec Resources

SIS Web

• SIS web is a useful tool for determining the isotope distribution within mass spectroscopy given the chemical formula.
  SIS Web
  

  
  
  

Mobile Apps

Oligo Property

• Oligo Property is an app that will allow you to calculate a lot of oligonucleotide properties such as extinction coefficient, predicted mass etc. on the go. (Compatible with iOS)
  Oligo Property
  

  
  

Daily Calcs

• DailyCalcs is an app that can perform a number of useful lab-based calculations. (Compatible with iOS)
  Daily Calcs
  

Online Tutorials

Mestrelab Mnova




• This site contains a range of resources and tutorials to help in using the Mnova software suite, which the Tucker group use to analyse NMR data
  Mestrelab Mnova
  

BASI DigiSim




• This site contains a range of tutorials which cover the use of the DigiSim software package, which the Tucker group use to simulate cyclic voltammograms.
  BASI DigiSim