QuadPredict
QuadPredict provides a web service that predicts the stability of unmeasured G-quadruplexes. The service is based on a published Bayesian prediction framework [ref]. The framework utilizes experimental results provided by the quadruplex research community. Currently (Dec 2009), there are around 250 G-quadruplex experimental results in our database. The accuracy of the prediction increases as more experimental results are available. As such, we also provided a data entry service for the research community to contribute their experimental results. We also provided a simple querying service for the community to check on existing data and help in avoiding duplications. Details on each section are provide below.
Melting temperature (Tm) prediction
This service provides a prediction on the melting temperature of G-quadruplexes based on the sequences and cation concentrations alone. Currently, cations considered are K+, Na+, Mg2+, and NH4+.
Help/Tutorial - The data required is the G-quadruplex sequence (e.g. GGGTTGGGTTTGGGTTGGG) and the cation concentration (e.g. K+, 100 mM). The G-quadruplex sequence is to be entered in the 'Sequence(s)' text field. You may provide more than one sequence by separating each sequence into different line (i.e. using [enter]). The cation concentration may be changed by the value (in mM) on each of the separate fields below the 'Sequence(s)' text field. You can also get a prediction example by clicking on the 'Example' button at the bottom of the form. The prediction results are given as the melting temperature together with a standard deviation in our prediction.
Predict melting temperature here
Data view
In order to avoid duplication of effort experimental works, we provide a simple query service on the data provided by the research community currently used in our prediction service.
Help/Tutorial - The only data required is the G-quadruplex sequence of interest (e.g. GGGTTGGGTTTGGGTTGGG). You may perform the query on G-quadruplex sequences that either [i] contain the given sequence, or [ii] match exactly to the given sequence. This may be done by using the 'Exact sequence' option. Checking this option will only list G-quadruplexes that match exactly the given sequence.
Data entry
We provide a data entry page for the research community to contribute their experimental results directly into our database. This can be done by entering individual experimental result manually, or done in batch by uploading a CSV file. The template CSV can be downloaded here. You are required to register an account before entering/uploading your data, so that we can maintain the quality of the data.
Help/Tutorial - Help is available at the data entry page.
Website provided as a service to the quadruplex community by Han-Min Wong, Simon Rodgers and Julian Huppert, University of Cambridge.
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