Problem with SLiMFinder bioware webserver

There is currently a problem with the SLiMFinder webserver hosted at UCD, where masking is failing to be performed, regardless of settings. This severely impacts the quality of results. (Disorder, low complexity and n-terminal methionine masking are generally recommended for SLiMFinder.)

I am in communication with the Shields lab to try and get the issue fixed but, until it has been rectified, the bioware.ucd.ie SLiMFinder webserver should not be used.

If you wish to run SLiMFinder online, you can do so via the SLiMFinder REST server (see BioInfoSummer 2016 workshop), which can also be run from within Cytoscape using the SLiMScape App.

SLiMSuite bug with combined sequence case and disorder masking

A small flaw has been discovered in the current implementation of disorder masking when it is combined with masking upper or lower case residues (casemask=X dismask=T). Rather than predicting disorder on the unmasked sequence and then combining with any case masking, disorder predictions are currently made on the masked sequences.

Hopefully, this will have minimal impact for the majority of cases. (Although I am not certain, I suspect that it will produce a tendency to over-predict disorder and thus under-mask.) This bug has been fixed for the next release of SLiMSuite. Note that other masking combinations are not affected.