SLiMSuite release v1.2.0 (2016-09-12) online

The long-overdue September 2016 release of SLiMSuite 2016-09-12 - v1.2.0 is now on GitHub. Apart from a few bug fixes, the main updates in this release are to the tools for PacBio genomics, notably PAGSAT, SMRTSCAPE and a new SNP Mapping tool, Snapper. These are still in development and need further documentation but are ready for use with a little help. Please get in touch if you are interested. Proper documentation and example use will hopefully follow soon, as the first PacBio yeast paper is written.

GABLAM has had some minor tweaks for improved function with Snapper, PAGSAT and another developmental tool that will be in the next release (REVERT - available via the REST servers). These have been focused on the fragfas=T output of fragmented BLAST hits based on local alignments. This includes addition of a new default to reverse complement reverse hits (fragrevcomp=T) and the separation of parameters for splitting up local hits into multiple fragments (gablamfrag=X) and merging close/overlapping fragments (fragmerge=X).

SLiMSuite updates in this release

Updates in extras/:

• rje_pydocs: Updated from Version 2.16.2.
→ Version 2.16.3: Fixed docstring REST parsing to work with _V* modules.

Updates in libraries/:

• rje: Updated from Version 4.15.1.
→ Version 4.16.0: Added list2dict(inlist,inkeys) and dict2list(indict,inkeys) functions.
→ Version 4.16.1: Improved handling of integer parameters when given bad commands.
→ Version 4.17.0: Added extra functions to randomList()

• rje_blast_V2: Updated from Version 2.9.1.
→ Version 2.10.0: Added nocoverage calculation based on local alignment table.
→ Version 2.11.0: Added localFragFas output method.
→ Version 2.11.1: Fixed snp local table revcomp bug. [Check this!]
→ Version 2.11.2: Fixed GABLAM calculation bug when '*' in protein sequences.

• rje_db: Updated from Version 1.8.0.
→ Version 1.8.1: Added sfdict to saveTable output.

• rje_genbank: Updated from Version 1.3.2.
→ Version 1.4.0: Added addtags=T/F : Add locus_tag identifiers if missing - needed for gene/cds/prot fasta output [False]
→ Version 1.4.1: Fixed genetic code warning.
→ Version 1.5.0: Added setupRefGenome() method based on PAGSAT code.
→ Version 1.5.1: Fixed logskip append locus sequence file bug.
→ Version 1.5.2: Fixed addtag(s) bug.

• rje_hprd: Updated from Version 1.2.
→ Version 1.2.1: Fixed "PROTEIN_ARCHITECTURE" bug.

• rje_menu: Updated from Version 0.3.
→ Version 0.4.0: Changed handling of default for exiting menu loop. May affect behaviour of some existing menus.

• rje_mitab: Updated from Version 0.2.0.
→ Version 0.2.1: Fixed redundant evidence/itype bug (primarily dip)

• rje_obj: Updated from Version 2.1.3.
→ Version 2.2.0: Added screenwrap=X.
→ Version 2.2.1: Improved handling of integer parameters when given bad commands.

• rje_samtools: Updated from Version 0.1.0.
→ Version 0.2.0: Added majmut=T/F : Whether to restrict output and stats to positions with non-reference Major Allele [False]
→ Version 1.0.0: Major reworking. Old version frozen as rje_samtools_V0.
→ Version 1.1.0: Added snptabmap=X,Y alternative SNPTable mapping and read_depth statistics []. Added majref=T/F.
→ Version 1.2.0: Added developmental combining of read mapping onto two different genomes.
→ Version 1.3.0: Major debugging and code clean up.
→ Version 1.4.0: Added parsing of read number (to link SNPs) and fixed deletion error at same time. Added rid=T/F and snponly=T/F.
→ Version 1.5.0: Added biallelic=T/F : Whether to restrict SNPs to pure biallelic SNPs (two alleles meeting mincut) [False]
→ Version 1.5.1: Fixed REF/Ref ALT/Alt bug.
→ Version 1.6.0: Added majfocus=T/F : Whether the focus is on Major Alleles (True) or Mutant/Reference Alleles (False) [True]
→ Version 1.7.0: Added parsing of *.sam files for generating RID table.
→ Version 1.8.0: Added read coverage summary/checks.
→ Version 1.8.1: Fixed issue when RID file not generated by pileup parsing. Set RID=True by default to avoid issues.

• rje_samtools_V0: Created/Renamed/moved.
→ Version 0.0: Initial Compilation.
→ Version 0.1.0: Modified version to handle multiple loci per file. (Original was for single bacterial chromosomes.)
→ Version 0.2.0: Added majmut=T/F : Whether to restrict output and stats to positions with non-reference Major Allele [False]

• rje_seq: Updated from Version 3.23.0.
→ Version 3.24.0: Added REST seqout output.

• rje_seqlist: Updated from Version 1.15.3.
→ Version 1.15.4: Fixed REST server output bug.
→ Version 1.15.5: Fixed reformat=fasta default issue introduced from fixing REST output bug.
→ Version 1.16.0: Added edit=T sequence edit mode upon loading (will switch seqmode=list).
→ Version 1.17.0: Added additional summarise=T output for seqmode=db.
→ Version 1.18.0: Added revcomp to reformat options.
→ Version 1.19.0: Added option log description for deleting sequence during edit.
→ Version 1.20.0: Added option to give a file of changes for edit mode.
→ Version 1.20.1: Fixed edit=FILE deletion bug.

• rje_sequence: Updated from Version 2.5.2.
→ Version 2.5.3: Fixed genetic code warning error.

• rje_slimcore: Updated from Version 2.7.5.
→ Version 2.7.6: Added feature masking log info or warning.
→ Version 2.7.7: Switched feature masking OFF by default to give consistent Uniprot versus FASTA behaviour.

• rje_synteny: Created/Renamed/moved.
→ Version 0.0.0: Initial Compilation.

• rje_taxonomy: Updated from Version 1.1.0.
→ Version 1.2.0: Added storage of Parents.

• rje_tree: Updated from Version 2.13.0.
→ Version 2.14.0: Added cladeSpec().

• rje_uniprot: Updated from Version 3.21.4.
→ Version 3.22.0: Tweaked REST table output.

• rje_xref: Updated from Version 1.8.0.
→ Version 1.8.1: Added rest run mode to avoid XRef table output if no gene ID list is given. Added `genes` and `genelist` as `idlist=LIST` synonym.
→ Version 1.8.2: Catching self.dict['Mapping'] error for REST server.

• snp_mapper: Updated from Version 0.4.0.
→ Version 0.5.0: Added CDS rating.
→ Version 0.6.0: Added AltFT mapping mode (map features to AltLocus and AltPos)
→ Version 0.7.0: Added additional fields for processing Snapper output. (Hopefully will still work for SAMTools etc.)
→ Version 0.8.0: Added parsing of GFF file from Prokka.
→ Version 0.8.1: Corrected "intron" classification for first position of features. Updated FTBest defaults.
→ Version 1.0.0: Version that works with Snapper V1.0.0. Not really designed for standalone running any more.

Updates in tools/:

• comparimotif_V3: Updated from Version 3.12.
→ Version 3.13.0: Added REST server function.

• gablam: Updated from Version 2.20.0.
→ Version 2.21.0: Added nocoverage Table output of regions missing from pairwise SNP Table.
→ Version 2.21.1: Added fragrevcomp=T/F : Whether to reverse-complement DNA fragments that are on reverse strand to query [True]
→ Version 2.22.0: Added description to HitSum table.
→ Version 2.22.1: Added localaln=T/F to keep local alignment sequences in the BLAST local Table.
→ Version 2.22.2: Fixed local output error. (Query/Qry issue - need to fix this and make consistent!)
→ Version 2.22.3: Fixed blastv and blastb error: limit also applies to individual pairwise hits!
→ Version 2.23.0: Divided GablamFrag and FragMerge.

• pagsat: Updated from Version 1.6.1.
→ Version 1.7.0: Added tidy=T/F option. (Development)
→ Version 1.7.1: Updated tidy=T/F to include initial assembly.
→ Version 1.7.2: Fixed some bugs introduced by changing gablam fragment output.
→ Version 1.7.3: Added circularise sequence generation.
→ Version 1.8.0: Added orphan processing and non-chr naming of Reference.
→ Version 1.9.0: Modified the join sorting and merging. Added better tracking of positions when trimming.
→ Version 1.9.1: Added joinmargin=X : Number of extra bases allowed to still be considered an end local BLAST hit [10]
→ Version 1.10.0: Added weighted tree output and removed report warning.
→ Version 1.10.1: Fixed issue related to having Description in GABLAM HitSum tables.
→ Version 1.10.2: Tweaked haploid core output.
→ Version 1.10.3: Fixed tidy bug for RevComp contigs and switched joinsort default to Identity. (Needs testing.)
→ Version 1.10.4: Added genetar option to tidy out genesummary and protsummary output. Incorporated rje_synteny.
→ Version 1.10.5: Set gablamfrag=1 for gene/protein hits.
→ Version 1.11.0: Consolidated automated tidy mode and cleaned up some excess code.
→ Version 1.11.1: Added option for running self-PAGSAT of ctidX contigs versus haploid set. Replaced ctid "X" with "N".
→ Version 1.11.2: Fixed Snapper run choice bug.

• pingu_V4: Updated from Version 4.5.3.
→ Version 4.6.0: Added hubonly=T/F : Whether to restrict pairwise PPI to those with both hub and spoke in hublist [False]
→ Version 4.6.1: Fixed some ppifas=T/F bugs and added combineppi=T/F : Whether to combine all spokes into a single fasta file [False]
→ Version 4.6.2: Added check/filter for multiple SpokeUni pointing to same sequence. (Compilation redundancy mapping failure!)
→ Version 4.6.3: Fixed issue with 1:many SpokeUni:Spoke mappings messing up XHub.
→ Version 4.7.0: Added ppidbreport=T/F : Summary output for PPI compilation of evidence/PPIType/DB overlaps [True]
→ Version 4.8.0: Fixed report duplication issue and added additional summary output

• qslimfinder: Updated from Version 2.1.0.
→ Version 2.1.1: Switched feature masking OFF by default to give consistent Uniprot versus FASTA behaviour.

• seqsuite: Updated from Version 1.11.0.
→ Version 1.11.1: Redirected PacBio to call SMRTSCAPE.
→ Version 1.11.2: Fixed batchrun batchlog=False log error.
→ Version 1.12.0: Added Snapper.

• slimfarmer: Updated from Version 1.4.3.
→ Version 1.4.4: Modified default vmem request to 126GB from 127GB.
→ Version 1.4.5: Updated BLAST loading default to 2.2.31

• slimfinder: Updated from Version 5.2.1.
→ Version 5.2.2: Added warnings for ambocc and minocc that exceed the absolute minima. Updated docstring.
→ Version 5.2.3: Switched feature masking OFF by default to give consistent Uniprot versus FASTA behaviour. Fixed FTMask=T/F bug.

• slimparser: Updated from Version 0.3.3.
→ Version 0.3.4: Tweaked error messages.
→ Version 0.4.0: Added simple json format output.

• slimprob: Updated from Version 2.2.4.
→ Version 2.2.5: Fixed FTMask=T/F bug.

• slimsearch: Updated from Version 1.7.
→ Version 1.7.1: Minor modification to docstring. Preparation for update to SLiMSearch 2.0 optimised for proteome searches.

• slimsuite: Updated from Version 1.5.1.
→ Version 1.5.2: Updated XRef REST call.
→ Version 1.6.0: Removed SLiMCore as default. Default will now show help.

• smrtscape: Updated from Version 1.8.0.
→ Version 1.9.0: Updated empirical preassembly mapefficiency calculation.
→ Version 1.10.0: Added batch processing of subread files.
→ Version 1.10.1: Fixed bug in batch processing.

• snapper: Created/Renamed/moved.
→ Version 0.0.0: Initial Compilation.
→ Version 0.1.0: Tidied up with improved run pickup.
→ Version 0.2.0: Added FASTQ and improved CNV output along with all features.
→ Version 0.2.1: Fixed local output error. (Query/Qry issue - need to fix this and make consistent!) Fixed snp local table revcomp bug.
→ Version 0.2.2: Corrected excess CNV table output (accnum AND shortname).
→ Version 0.2.3: Corrected "intron" classification for first position of features. Updated FTBest defaults.
→ Version 1.0.0: Working version with completed draft manual. Added to SeqSuite.
→ Version 1.0.1: Fixed issues when features missing.

SLiMSuite release 2015-01-07 now available

A new download of SLiMSuite (release 2015-01-07) is now available at both UK (U. Southampton) and Australia (UNSW) sites (svn r613).

Many of the changes are under the hood, in preparation for a new set of REST services, which will be coming soon. The new download also features two new programs in the tools/ folder, which will hopefully simplify running many of the programs. The core programs and several of the key accessory programs (e.g. rje_seq and rje_uniprot) can now be run using the main SLiMSuite program:

python tool/slimsuite.py -prog X

where X is one of the SLiMSuite or SeqSuite programs. To see which are currently supported, run with -help. Simply add additional commandline options for the chosen program (and/or use ini files) as normal. For program-specific help, run with help=T: this will give the help documentation for program X rather than SLiMSuite. (NB. SLiMSuite can be used to access both SLiMSuite and SeqSuite programs. There is also a seqsuite.py that can be used to access just the SeqSuite programs and accessories.)

The other major update is that SLiMSuite programs (SLiMProb, SLiMFinder, QSLiMFinder and SLiMCore) can now take lists of Uniprot accession numbers as alternative input, using uniprotid=LIST in place of seqin=FILE. Providing there is an open internet connection, the relevant proteins will be downloaded from the Uniprot server for analysis.

GABLAM has also benefited from the addition of a new fullblast=T mode, which will perform the full all versus all BLAST+ search prior to GABLAM processing. Depending on your machine setup, this can be faster than the current method that forks out a single sequence at a time and is more IO-intensive as a result. The GABLAM functions to use existing BLAST+ results have also been fixed and tidied a little. (If re-running might be required, keepblast=T can retain the full BLAST results file to accelerate subsequent runs.)

Updates since last release:

• fiesta: Updated from Version 1.8.
→ Version 1.8.1: Replaced type with stype throughout to try and avoid TypeError crashes.
→ Version 1.9.0: Altered HAQDB to be a list of files rather than just one.

• gablam: Updated from Version 2.14.
→ Version 2.15.0: Added seqnr function. Add run() method.
→ Version 2.16.0: Added fullblast=T/F : Whether to perform full BLAST followed by blastres analysis [False]
→ Version 2.16.1: Fixed a bug where the fullblast option was failing to return scores and evalues.

• multihaq: Updated from Version 1.1.
→ Version 1.2: Changed defaults to autoskip=F.

• pingu_V4: Updated from Version 4.2.
→ Version 4.3: Modified to use Pfam as hub field for DomPPI generation. Modified naming of PPI output after ppisource.

• seqsuite: Created/Renamed.
→ Version 0.0: Initial Compilation.
→ Version 0.1: Added rje_seq and FIESTA. Added Uniprot.
→ Version 1.0: Moved to tools/ for general release. Added HAQESAC and MultiHAQ. Moved mod to enable easy external access.
→ Version 1.1: Added XRef = rje_xref.XRef. Identifier cross-referencing module.
→ Version 1.2: Added taxonomy.
→ Version 1.3.0: Added rje_zen.Zen. Modified code to work with REST services.
→ Version 1.4.0: Added rje_tree.Tree, GABLAM and GOPHER.

• slimbench: Updated from Version 2.5.
→ Version 2.6: Added ELM domain interactions table: http://www.elm.eu.org/infos/browse_elm_interactiondomains.tsv.
→ Version 2.6: Fixed issues introduced with new SLiMCore V2.0 SLiMSuite code.
→ Version 2.7: Reinstate filtering. (Not sure why disabled.) Add genspec=LIST to filter by species. Added domlink=T/F.
→ Version 2.8.0: Implemented PPIBench benchmarking for datasets without Motifs in name.

• slimfarmer: Updated from Version 1.3.
→ Version 1.4: Added modules=LIST : List of modules to add in job file [clustalo,mafft]
→ Version 1.4.1: Fixed farm=batch mode for qsub=T.

• slimmaker: Updated from Version 1.1.
→ Version 1.2.0: Modified to work with REST servers

• slimmutant: Updated from Version 1.0.
→ Version 1.1: Minor tweaks to generate method to increase speed. (Make index in method.) Added splitfield=X.
→ Version 1.2: Added a batch mode for mutfiles - all other options will be kept fixed. Added maxmutant and minmutant.
→ Version 1.3: Added SLiMPPI analysis (will set analyse=T). Started basing on SLiMCore

• slimprob: Updated from Version 2.1.
→ Version 2.2.0: Added basic REST functionality.

• slimsuite: Created/Renamed.
→ Version 0.0: Initial Compilation based on SeqSuite.
→ Version 1.0: Moved to tools/ for general release. Added reading and using of SeqSuite programs.
→ Version 1.1: Added slimlist.
→ Version 1.2: Added SLiMBench.
→ Version 1.3.0: Added SLiMMaker and modified code to work with REST services.

• rje: Updated from Version 4.12.
→ Version 4.13.0: Added new built-in attributes/options for REST services.
→ Version 4.13.1: Fixed MemSaver typo in WarnLog output. Modified mkDir() to avoid clashes raising errors.

• rje_db: Updated from Version 1.5.
→ Version 1.6: Added option to save a subset of entries using saveToFile(savekeys=LIST).
→ Version 1.7.0: Added splitchar to table splitting.
→ Version 1.7.1: Reinstated raise error if expected table missing.

• rje_dismatrix_V3: Created/Renamed.
→ Version 3.0: Updated to new rje_obj.RJE_Object class.

• rje_ensembl: Updated from Version 2.13.
→ Version 2.14: Add enspep=T/F : Create full gnspacc EnsEMBL peptide datasets [False]

• rje_genbank: Added to download.
→ Version 0.0: Initial Compilation.
→ Version 0.1: Modified and Tidied output a little.
→ Version 0.2: Added details to skip and option to use different detail for protein accession number.
→ Version 0.3: Added reloading of features.
→ Version 1.0: Basic functioning version. Added fetchuid=LIST Genbank retrieval to generate seqin=FILE.
→ Version 1.1: Added use of rje_taxonomy for getting Species Code from TaxID.
→ Version 1.2: Modified to deal with genbank protein entries.
→ Version 1.2.1: Fixed feature bug that was breaking parser and removing trailing '*' from protein sequences.
→ Version 1.2.2: Fixed more features that were breaking parser.

• rje_obj: Updated from Version 2.0.
→ Version 2.1.0: Added new built-in attributes/options for REST services.

• rje_ppi: Updated from Version 2.8.
→ Version 2.8.1: Fixed bug with Spring Layout interruption message.

• rje_qsub: Updated from Version 1.5.
→ Version 1.6: Added modules=LIST : List of modules to add in job file [clustalo,mafft]
→ Version 1.6.1: Added R/3.1.1 to modules.

• rje_seq: Updated from Version 3.20.
→ Version 3.21.0: Added extraction of uniprot IDs for seqin.

• rje_seqlist: Updated from Version 1.7.
→ Version 1.8: Added sortseq=X : Whether to sort sequences prior to output (size/invsize/accnum/name/seq/species/desc) [None]
→ Version 1.9.0: Added extra functions for returning sequence AccNum, ID or Species code.
→ Version 1.10.0: Added extraction of uniprot IDs for seqin. Added more dna2prot reformatting options.

• rje_sequence: Updated from Version 2.3.
→ Version 2.4: Added recognition of modified IPI format. Added standalone low complexity masking.
→ Version 2.4.1: Moved the gnspacc fragment recognition to reduce issues. Should perhaps remove completely?

• rje_slim: Updated from Version 1.8.
→ Version 1.9: Reinstated ambcut for slimToPattern()

• rje_slimcalc: Updated from Version 0.8.
→ Version 0.9: Improvements to use of GOPHER.

• rje_slimcore: Updated from Version 2.2.
→ Version 2.3: Docstring edits. Minor tweak to walltime() to close open files.
→ Version 2.4: Added megaslimfix=T/F : Whether to run megaslim in "fix" mode to tidy/repair existing files [False]
→ Version 2.5: Added (hidden) slimmutant=T/F : Whether to ignore '.p.\D\d+\D' at end of accnum. Made default append=True.
→ Version 2.6.0: Added uniprotid=LIST : Extract IDs/AccNums in list from Uniprot into BASEFILE.dat and use as seqin=FILE. []
→ Version 2.6.1: Removed the maxseq default setting.

• rje_slimlist: Updated from Version 1.4.
→ Version 1.5: Added run() method for slimsuite.py compatibility. Improved split motif handling.
→ Version 1.6: Modified to read in new ELM class download file with extra header information. Added varlength=T/F filter.
→ Version 1.6: Modified so that filtering one element of a split motif removes all.

• rje_tree: Updated from Version 2.10.
→ Version 2.11.0: Modified for standalone running as part of SeqSuite.

• rje_uniprot: Updated from Version 3.19.
→ Version 3.20: Updated dbsplit=T output and checked function with Pfam. Probably needs work for other databases.
→ Version 3.20.1: Added uniprotid=LIST as an alias to acclist=LIST and extract=LIST.
→ Version 3.20.2: Added extra sequence return methods to UniprotEntry. Added fasta REST output.
→ Version 3.20.3: Fixed bug if new uniprot extraction method fails.

• rje_xml: Created/Renamed.
→ Version 0.0: Initial Compilation.
→ Version 0.1: Added xml.sax functions.
→ Version 0.2: Added parsing from URL.

• rje_xref: Updated from Version 1.1.
→ Version 1.2: Added join=LIST Run in join mode for list of FILE:key1|...|keyN:JoinField [] and naturaljoin=T/F.
→ Version 1.3.0: Added compress=LIST to handle 1:many input data. []

• rje_zen: Updated from Version 1.2.
→ Version 1.3.0: Modified output to work with new REST service calls.

SLiMSuite servers and programs

An emerging field of biology is the role of intrinsically disordered regions in protein function and, specifically, protein-protein interactions (PPI) [1-2]. Of particular interest, Short, Linear Motifs (SLiMs) playing a vital role in disorder-mediated PPI, acting as ligands for molecular signalling, post-translational modifications and subcellular targeting [3]. SLiMs have extremely compact protein interaction interfaces, generally encoded by less than 4 major affinity-/specificity-determining residues within a stretch of 2-10 residues [4]. Their small size enables high functional density and evolutionary plasticity, which is frequently exploited by rapidly evolving pathogens that use them to hijack cellular processes [5]. These same features also make experimental discovery a challenge and considerable attention has therefore been given to computational methods for SLiM prediction and analysis [6].

A number of these tools have been developed by the Edwards and Shields labs [7-11] and made available as part of the SLiMSuite package and online as webservers (http://bioware.ucd.ie) [9-10,12-14], with two new tools, SLiMPrints and QSLiMFinder, currently in preparation for submission, and SLiMMaker to be added soon. The main tools that form the SLiMSuite package/servers are as follows:

• SLiMFinder [8,13]: de novo SLiM prediction based on a statistical model of over-represented motifs in unrelated proteins.
  
• SLiMDisc [7,12]: de novo SLiM prediction based on heuristic ranking of over-represented motifs in unrelated proteins.
  
• SLiMPred [11]: de novo SLiM/MoRF prediction in single proteins based machine learning of motif attributes.
  
• SLiMSearch [10]: biological context (disorder & conservation) for searches of pre-defined motifs with under- and over-representation statistics, correcting for evolutionary relationships.
  
• SLiMSearch 2.0 [14]: biological context (disorder & conservation) and ranking for proteome-wide searches of pre-defined motifs.
  
• SLiMPrints (in prep.): de novo SLiM/MoRF prediction in single proteins from statistical clustering of conserved disordered residues.
  
• QSLiMFinder (server coming soon): Query-based variant of SLiMFinder with increased sensitivity and specificity.
  
• CompariMotif [9]: Motif-motif comparison tool.
  
• SLiMMaker (coming soon): Simple tool for converting aligned peptides or SLiM occurrences into a regular expression motif.
  
• GOPHER [12]: Automated orthologue prediction and alignment algorithm. Used for conservation-based masking (SLiMFinder/SLiMSearch) and prediction (SLiMPrints).
  
• GABLAM [7] (server coming soon): BLAST-based protein similarity scoring and clustering. Used for SLiMFinder and SLiMSearch adjustments for evolutionary relationships.
  

Personnel (and funding applications) permitting, a number of improvements for these resources are planned, including updates to the underlying databases for proteome-wide predictions (SLiMSearch 1.0 & 2.0), conservation analyses (SLiMSearch 1.0 & 2.0, SLiMPrints, GOPHER) and SLiM comparisons (CompariMotif). We also intend to improve the integration of different tools, allowing seamless continuation of analyses. Motif predictions ((Q)SLiMFinder/SLiMPrints/SLiMPred) will be able to be searched directly against known motifs (CompariMotif) or proteomes (SLiMSearch); GOPHER alignments will be accessible for SLiMPrints analyses and even SLiMSearch/(Q)SLiMFinder input; outputs of motif occurrences ((Q)SLiMFinder/SLiMSearch) can be used to redefine motifs using SLiMMaker etc. If you have any other suggestions for improvements, please let us know.


References:

[1] Tompa P (2011) Unstructural biology coming of age. Curr Opin Struct Biol 21: 419; [2] Babu MM et al. (2011) Intrinsically disordered proteins: regulation and disease. Curr Opin Struct Biol 21:432; [3] Diella F et al. (2008) Understanding eukaryotic linear motifs and their role in cell signaling and regulation. Front Biosci 13:6580; [4] Davey NE et al. (2012) Attributes of short linear motifs. Mol Biosyst 8:268; [5] Davey NE, Trave G & Gibson TJ (2011) How viruses hijack cell regulation. Trends Biochem Sci 36:159; [6] Davey NE, Edwards RJ & Shields DC (2010) Computational identification and analysis of protein short linear motifs. Front Biosci 15:801; [7] Davey NE, Shields DC & Edwards RJ (2006): SLiMDisc: short, linear motif discovery, correcting for common evolutionary descent. Nucleic Acids Res. 34:3546; [8] Edwards RJ, Davey NE & Shields DC (2007): SLiMFinder: A probabilistic method for identifying over-represented, convergently evolved, short linear motifs in proteins. PLoS ONE 2:e967; [9] Edwards RJ, Davey NE & Shields DC (2008): CompariMotif: Quick and easy comparisons of sequence motifs. Bioinformatics 24:1307; [10] Davey NE et al. (2010): SLiMSearch: a webserver for finding novel occurrences of short linear motifs in proteins, incorporating sequence context. Lecture Notes in Bioinformatics 6282:50; [11] Mooney C et al. (2012): Prediction of short linear protein binding regions. J Mol Biol 415:193; [12] Davey NE, Edwards RJ & Shields DC (2007): The SLiMDisc server: short, linear motif discovery in proteins. Nuc Acids Res 35:W455; [13] Davey NE et al. (2010): SLiMFinder: a web server to find novel, significantly over-represented, short protein motifs. Nuc Acids Res 38:W534; [14] Davey NE et al. (2011): SLiMSearch 2.0: biological context for short linear motifs in proteins. Nuc Acids Res 39:W56.