Tuesday 21 August 2012

CompariMotif V3.6

Both the webserver and SLiMSuite download have now been updated to CompariMotif Version 3.6.

One of the main changes over earlier versions of CompariMotif is that ELM Class exports can now be used directly as input. Any tab-delimited file (*.tdt or *.tsv) with a "Regex" field header will be recognised and motifs extracted using the ELMIdentifier, Regex and Description fields.

To handle some of the more complex motifs now in ELM, the motif splitting function has also been expanded and strengthened. (The caveat is the small bug in the current download which will be fixed in the next release.) In addition to either/or regex elements, variable length non-wildcards are now recognised and will be reformatted for CompariMotif searching.

For example:
Motif [IL]{1,2}[^P].(RG|K)
will be split to form:
Motif_a [IL][^P].RG
Motif_b [IL][^P].K
Motif_c [IL][IL][^P].RG
Motif_d [IL][IL][^P].K
The descriptions will also be appended with "Version 1", "Version 2" etc.

The final minor update replaces ? in motif Regex patterns with .{0,1}. As it uses the same modules for motif input, these changes will also affect SLiMSearch input but not (yet) be taken into consideration for the SLiMChance statistics.

Note. The 2008 version of ELM on the bioware server was manually split and therefore the suffixes added by CompariMotif for later versions of ELM will not necessarily match up.

Monday 20 August 2012

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.)

Saturday 18 August 2012

Bioware servers back up

Following the recent move-induced technical issues, the Bioware webservers are now back on line, with the exception of SLiMSearch 1.0. SLiMSearch2 is also operating with reduced function until another upgrade can be performed in the near future. CompariMotif has been upgraded to Version 3.6 in line with the recent package updates.

A few of the links to help pages etc. might still be broken, so please report anything that is not quite behaving as expected.

Friday 17 August 2012

New software downloads available

SLiMsuite and SeqSuite downloads have now been updated and are available from my homepage.

The only real change of note since the last release is that CompariMotif can now recognise ELM Class downloads and the motif splitting has been updated to cope with variable-length non-wildcard repeats (e.g. R{0,1}).

The CompariMotif webserver is undergoing some final checks and should be back up shortly, with SLiMFinder and SLiMSearch to follow.

Saturday 11 August 2012

SLiMSuite servers temporarily down

Following some technical issues that have arisen due to some quite major behind-the-scenes re-organisation, the Bioware webserver implementations of SLiMSuite programs have been temporarily taken off-line.

The plan is to give them a bit of attention, iron out any wrinkles that have developed, and then hopefully get them back online over the next week or so. The servers affected are:
  • CompariMotif
  • SLiMDisc (now part of SLiMFinder)
  • SLiMFinder
  • SLiMSearch
  • SLiMSearch 2.0
These programs (except SLiMSearch 2.0) are available for download. If you have a particular need for any of these servers, please contact me and I will accelerate its re-appearance.

As each server becomes available, it will be posted here.

Friday 10 August 2012

Bioware servers behaving erratically

The SLiMSuite servers housed at bioware.ucd.ie are currently behaving a bit strangely. This is under investigation and we hope to have it sorted out soon. If you spot any odd or unexpected behaviour with the servers, please let us know.