10/03/2015 - ViennaRNA package updated
We updated the software to last version (2.1.9). This update may change a litle your previous results. Specially referring to the free energy of the IREs predicted.
31/12/2012 - This is SIREs Server version 2.0
The updated version includes a "batch mode" enabling larger submissions up to thousands of sequences and millions of residues, to predict IREs.
This batch server is several times faster than the interactive one and can process thousand of sequences in minutes. However this speed comes at the cost of the detailed output available in the interactive mode, to comply with computational demands.
The batch server provides a list of predicted IREs in table format to browse the results, and the same results in GFF format to download.
However, from the browsable table you can select up to 10 sequences for direct submission to the interactive server where you will get the detailed results you are used to. You have an example output here to try it.
In addition, a novel motif, the motif 19 (8-CNNNNNAAGUUN-19) has been added to the predictor. You can see and example here
We have updated the FAQ Section to include this information
The Reference section now includes a link to the list of papers that cite the SIRES NAR paper.