Welcome to the MASTR server

Multiple Alignment of STructural RNAs

This webserver performs multiple alignment and secondary structure prediction on a set of structural RNA sequences using the MASTR program. It is hosted by The Bioinformatics Center at the University of Copenhagen in Denmark. Questions, bugs etc. should be emailed to Stinus Lindgreen.

To use the MASTR webserver, simply upload your RNA sequences (i.e. at least 2) in FASTA format either as a file or by pasting them into the box below. You will receive an email when the results are ready.

If you use this service, please add a reference to our paper:
S. Lindgreen, P.P. Gardner and A. Krogh (2007): MASTR: Multiple alignment and structure prediction of non-coding RNAs using simulated annealing, Bioinformatics, 23(24):3304-11 [Link to paper]

You can download the source code and various data files here.

Dataset with RNA sequences (i.e. at least 2) in Fasta format
Advanced parameters:
Gap open probability
Gap extension probability
Base pairing null probability
Scaling factor of basepairing probability
Scaling factor of log-likelihood
Scaling factor of covariation
Covariation cut-off
Iteration dependence on alignment size (#nucl.)
Iteration dependence on alignment length

Email notification (when done):