New SLiMSuite, SeqSuite and RJESuite releases are now available

New releases of SLiMSuite, SeqSuite and RJESuite are now available from the Edwards Lab software page.

Please note that the documentation (particularly the manuals) are still lagging a bit behind, so do report anything that does not make sense. The default settings also need to be verified as there is a chance that some of these may have inadvertently changed over the years. (The same core code is now used for the webservers, which often have different defaults.) Checking these along with updating and checking the servers themselves are ongoing priorities.

A full list of updated modules is given below. As well as SLiMMaker now handling end of sequence characters, the biggest changes this release are updates to CompariMotif to (3.7) output unmatched input motifs and (3.8) improve handling of partially overlapping ambiguous positions (e.g. [AGS] and [ST]). The motivation behind both these changes is the ongoing benchmarking (and preparation for publication) of QSLiMFinder and the creation of SLiMBench for benchmarking motif prediction methods. A QSLiMFinder section has been added to the SLiMFinder Manual (section 5.4). SLiMBench is still a work in progress and will be documented in a later release.

Updates since last release:

• comparimotif_V3: Updated from Version 3.6.
→ Version 3.7: Added coreIC and output of unmatched motifs.
→ Version 3.8: Added overlaps=T/F : Whether to include overlapping ambiguities (e.g. [KR] vs [HK]) as match [True]
→ Version 3.8: Changed scoring of overlapping ambiguities - uses IC of all possible ambiguities. Added "Ugly" match type.

• slimbench: Created.
→ Version 0.0: Initial Compilation.
→ Version 0.1: Functional version with benchmarking dataset generation.
→ Version 1.0: Consolidation of "working" version with additional basic benchmarking analysis.
→ Version 1.1: Added simulated dataset construction and benchmarking.
→ Version 1.2: Added MinIC filtering to benchmark assessment. Sorted beginning/end of line for reduced ELMs.
→ Version 1.3: Made SimCount a list rather than Integer. Sorted CompariMotif assessment issue.
→ Version 1.4: Added ICCut and SLiMLenCut as lists and output columns.
→ Version 1.5: Added Summary Results output table. Removed PropRes.

• slimmaker: Updated from Version 1.0.
→ Version 1.1: Modified to work with end of line characters.

• slimsearch: Updated from Version 1.5.
→ Version 1.6: Minor tweaks to Log output. Add option for UPC number in occ output.

• rje: Updated from Version 4.1.
→ Version 4.2: Modified INI reading across the board to look in ../settings/ and look for defaults.ini as well as rje.ini.
→ Version 4.2: Enabled handing on -ini FILE in addition to ini=FILE.
→ Version 4.3: Added ilist and nlist types to cmdRead for objects. (Lists of integers and floats). Add ratio() function.

• rje_blast: Updated from Version 1.13.
→ Version 1.14: Added blast.checkProg(qtype,stype) to check whether blastp setting matches sequence formats.

• rje_db: Created.
→ Version 0.0: Initial Compilation.
→ Version 0.1: Added merge tables option.
→ Version 0.2: Miscellaneous updates to various methods.
→ Version 0.3: Minor doc tweaks and added keepFields().

• rje_seq: Updated from Version 3.12.
→ Version 3.13: Updated sequence type checking for use with GABLAM 2.10.

• rje_seqlist: Created.
→ Version 0.0: Initial Compilation. Based on rje_seq 3.10.
→ Version 0.1: Added basic species filtering and sequence output.
→ Version 0.2: Added upper case filtering.
→ Version 0.3: Added accnum filtering and sequence renaming.
→ Version 0.4: Added sequence redundancy filtering.
→ Version 0.5: Added newgene=X for sequence renaming (newgene_spcode__newaccXXX). NewAcc no longer fixed Upper Case.
→ Version 1.0: Upgraded to "ready" Version 1.0. Added concatenate=T and split=X options for sequence concatenation.
→ Version 1.0: Added reading of sequence type from rje_seq.py and mixed=T/F.
→ Version 1.1: Added shortName() and modified SeqDict.

• rje_sequence: Updated from Version 2.0.
→ Version 2.1: Added re_unirefprot = re.compile('^([A-Za-z0-9\-]+)\s+([A-Za-z0-9]+)_([A-Za-z0-9]+)\s+')

• rje_slim: Updated from Version 1.5.
→ Version 1.6: Fixed splitting bug introduced by lower case motifs.

• rje_slimcore: Updated from Version 1.8.
→ Version 1.9: Minor modifications to Log output. Updated motifSeq() function to output unmasked sequences.

• rje_slimlist: Updated from Version 0.6.
→ Version 1.0: Functional module with lower case motif splitting fixed and ? -> .{0,1} replacement.

• rje_zen: Updated from Version 1.0.
→ Version 1.1: Added a few more words here and there.

Using SLiMFinder to discover "local motifs" in protein sequences

The makers of the highly successful MEME Suite have another tool out:

DLocalMotif: A discriminative approach for discovering local motifs in protein sequences

I've not had a chance to go over it in detail but it looks like it could be pretty useful, especially for subcellular targeting motifs. There is one thing that rankles me slightly, though. They define a "local motif" as

"patterns in DNA or protein sequences that occur in a short sequence interval relative to a sequence anchor or landmark."

They then go on to say:

"We believe that DLocalMotif is the only tool for discovering local motifs in protein sequences."

This is just a quick post to point out that SLiMFinder will happily find "local motifs" in protein sequences using the start and end of the sequence as an anchor or landmark. I think it is more limited than DLocalMotif as it is restricted to SLiMs that are very proximal to the sequence termini but it features the usual SLiMChance probability calculations and corrections for evolutionary relationships. (Even without restricting to searches relative to anchor points, SLiMFinder is very successful at finding the KDEL motif and C-terminal PDZ ligand motifs.) The max distance from the termini can be set by maxwild=X up to a limit of 9aa.

If you want to restrict yourself to just N- or C-terminal motifs, use the musthave=LIST option:

musthave="^" for N-terminal motifs.

musthave="$" for C-terminal motifs.

musthave="^,$" for both.

If you want to anchor the motifs internally, this can be done too with a bit of imagination. Just insert an non-standard amino acid character (e.g. Z) at the anchor position, set the expanded alphabet using alphabet=LIST and then force the motif to have the new symbol using musthave=X, e.g.:

alphabet="A,C,D,E,F,G,H,I,K,L,M,N,P,Q,R,S,T,V,W,Y,Z" musthave=Z

I must confess that I have never tried this but it should work and I am happy to help iron out any wrinkles.

You can also use position-specific or case masking to restrict motif analysis to certain regions of input proteins. This is probably even better than simply constraining the motif location, as it will reduce the sequence search space rather than the motif search space.

(BTW, SLiMFinder also has an experimental feature for using a negative dataset (negatives=FILE if anyone wants to try it out.)

SLiMMaker now handles end of sequence characters

SLiMMaker is a simple tool for generating regular expression motifs from aligned peptide sequences. It was originally made for making new SLiM definitions based on a set of aligned occurrences and therefore the ends of these peptides are typically not the actual ends of sequences. Sometimes, however, such as in the KDEL ER retrieval motif, they are at (or near) the end (or beginning) of a protein and you might want that taken into consideration when generating a motif.

The SLiMMaker website will now accept beginning (^) and end ($) of seuqence characters. The peptides still need to be aligned, so if using them you should fill in any non-conforming peptides with an X. If the peptides are of different lengths and the end of lines character ends up appearing within an ambiguous position with regular amino acids (e.g. [$AGS]), SLiMMaker will truncate the regular expression at that point (not including that position) - otherwise it just gets too messy!

This upgrade will appear in the next distributions of SLiMSuite and SeqSuite. As always, if it is not clear then just try it out with some test sequences. (And report any odd behaviour.)

SLiMPrints paper published

The SLiMPrints paper is now available online at Nucleic Acids Research (doi: 10.1093/nar/gks854; PMID: 22977176).

SLiMPrints: conservation-based discovery of functional motif fingerprints in intrinsically disordered protein regions

Davey NE, Cowan JL, Shields DC, Gibson TJ, Coldwell MJ, Edwards RJ.

Large portions of higher eukaryotic proteomes are intrinsically disordered, and abundant evidence suggests that these unstructured regions of proteins are rich in regulatory interaction interfaces. A major class of disordered interaction interfaces are the compact and degenerate modules known as short linear motifs (SLiMs). As a result of the difficulties associated with the experimental identification and validation of SLiMs, our understanding of these modules is limited, advocating the use of computational methods to focus experimental discovery. This article evaluates the use of evolutionary conservation as a discriminatory technique for motif discovery. A statistical framework is introduced to assess the significance of relatively conserved residues, quantifying the likelihood a residue will have a particular level of conservation given the conservation of the surrounding residues. The framework is expanded to assess the significance of groupings of conserved residues, a metric that forms the basis of SLiMPrints (short linear motif fingerprints), a de novo motif discovery tool. SLiMPrints identifies relatively overconstrained proximal groupings of residues within intrinsically disordered regions, indicative of putatively functional motifs. Finally, the human proteome is analysed to create a set of highly conserved putative motif instances, including a novel site on translation initiation factor eIF2A that may regulate translation through binding of eIF4E.

Server available at bioware.ucd.ie.

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.

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.)

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.