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.

Minor bug in GOPHER output with BLAST+

A bug has been identified with the current SLiMSuite release when using BLAST+ to generate orthologue alignments with GOPHER. Sequences extracted from the blast database have the first letter of their name truncated. In real terms, this should not make a lot of difference (if using the recommended naming format) but it could present mapping issues. A few other programs, such as HAQESAC, may also be affected if BLAST+ is being used to extract sequences.

A fix is available on request and will be part of the next release, which should be soon.

Missing gopher.py file

There is a bug with the current software download, with a file missing from the libraries/ directory. The download will hopefully be updated soon but in the meantime please email richard.edwards[at]unsw.ed.au and I will send you the file.

A note on using BLAST+ with SLiMSuite

One of the major changes in the last release was the incorporation of BLAST+ as a replacement for BLAST. It should be noted that BLAST+ has not been benchmarked with SLiMSuite and it is not clear how and when it will behave differently, particularly with regards to UPC generation (i.e. generating clusters of unrelated proteins).

Early indications are that BLAST+ has a greater tendency to return no hits for short sequences. This can cause issues with SLiMSuite programs if oldblast=F. This will be fixed in the next release but running with dev=T gets round this issue in the meantime.

Please note that UPC may be different with BLAST versus BLAST+. This will need to be the focus of further study.

QSLiMFinder 1.4: quicker and more efficient - available on request

The on-going benchmarking of QSLiMFinder has thrown up a couple of discoveries to date. The first is that, reassuringly, it appears to work. (More on this another time.) The second is that it is slow. Or, at least, it was slow.

Thankfully, the cause of its surprisingly slow performance (compared to SLiMFinder) has been tracked down and fixed. At the same time, a (related) potential memory issue with large query sequences has also been sorted out.

The underlying problem is unlikely to have had a large effect on the SLiM prediction itself, although this is currently under investigation. The last release of SLiMSuite was only last week and, as QSLiMFinder is not officially published and released yet, I will not be compiling a new download immediately to take advantage of the improvements. The revised code is available on request if anyone is using QSLiMFinder.

Minor bug in CompariMotif 3.6 download

The recent fixing up of the server has highlighted a couple of bugs that have crept in during the upgrading of CompariMotif to handle complex motifs better. (More on this in a later post.) The problem is restricted to lower case motifs, so stick to upper case and all will be well. It will be fixed in the next release. A replacement rje_slimlist.py file is available on request if anyone needs to fix it urgently. (This also features replacement of "?" characters with "{0,1}" so these motifs are no longer rejected.)