Links

DNA Resources

IDT Biophysics

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.

 

RiboTask

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.

 

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.

 

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.

 

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.

 

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.

 

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.


MASS SPEC RESOURCES

SIS Web

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


MOBILE APPS

Oligo Property

oligoproperty

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)

Daily Calcs

dailycalcs

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


ONLINE TUTORIALS

Mestrelab Mnova

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

BASI DigiSim

BASI

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.

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