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SLiMSuite SLiMFinder Server

# Output for SLiMFinder V5.2.2: Tue Dec 8 11:13:55 2015 # 1 warnings; 0 errors: see log output (below) for details. # JobID: 15120800001

Your SLiMFinder job has finished running and outputs have been parsed. Click on tabs to see server output. (Mouseover for description.)

The outfmt tab contains more information on the outputs. Click here for SLiMFinder help/documentation.

Content for individual tabs can be returned using &rest=X, where X is the tab name (e.g. &rest=log). Full output can be returned as text using &rest=full and parsed using SLiMParser:

python PATH/slimparser.py restin=JOBID restout=T [password=X] [restbase=X]

JobID 15120800001 (slimfinder) Finished.
IP:129.94.146.29
No queue.
slimfinder&uniprotid=LIG_PCNA_PIPBox_1&dismask=T
Run Started: 2015-12-08 11:13:55; PID=35116
Run finished: 2015-12-08 11:16:51

SLiMs and SLiMFinder

Short linear motifs (SLiMs) in proteins are functional microdomains of fundamental importance in many biological
systems. SLiMs typically consist of a 3 to 10 amino acid stretch of the primary protein sequence, of which as few
as two sites may be important for activity. SLiMFinder is a SLiM discovery program building on the principles of
the SLiMDisc software for accounting for evolutionary relationships between input proteins. This stops results
being dominated by motifs shared for reasons of history, rather than function. SLiMFinder runs in two phases:
(1) SLiMBuild constructs the motif search space based on number of defined positions, maximum length of "wildcard
spacers" and allowed amino acid ambiguities; (2) SLiMChance assesses the over-representation of all motifs,
correcting for the size of the SLiMBuild search space. This gives SLiMFinder high specificity.

Protein sequences can be masked prior to SLiMBuild. Disorder masking (using IUPred predictions) is highly
recommended. Other masking options are described in the manual and/or literature.

Running SLiMFinder

The standared REST server call for SLiMFinder is in the form:
slimfinder&uniprotid=LIST&dismask=T/F&consmask=T/F

Run with &rest=docs for program documentation and options. A plain text version is accessed with &rest=help.
&rest=OUTFMT can be used to retrieve individual parts of the output, matching the tabs in the default
(&rest=format) output. Individual OUTFMT elements can also be parsed from the full (&rest=full) server output,
which is formatted as follows:

###~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~###
# OUTFMT:
... contents for OUTFMT section ...

More options are available through the SLiMFinder server: http://www.slimsuite.unsw.edu.au/servers/slimfinder.php

After running, click on the main tab to see overall SLiM predictions. If any SLiMS have been predicted, the
occ tab will have details of which proteins (and where) they occur.

If no SLiMs are returned: [1] Try altering the masking settings. (Disorder masking is recommended. Conservation
masking can sometimes help but it depend on the dataset.) [2] Try relaxing the probability cutoff. Set
[probcut=1.0]{cmd:probcut} to see the best motifs, regardless of significance. (You may also want to reduce the [topranks=X]{cmd:topranks}
setting.)

Available REST Outputs

main = Main results table of predicted SLiM patterns (if any) [[extras=-1]{cmd:extras}]
occ = Occurrence table showing individual SLiM occurrences in input proteins [[extras=0]{cmd:extras}]
upc = List of Unrelated Protein Clusters (UPC) used for evolutionary corrections [[extras=0]{cmd:extras}]
cloud = Predicted SLiM "cloud" output, which groups overlapping motifs [[extras=1]{cmd:extras}]
seqin = Input sequence data [[extras=-1]{cmd:extras}]
slimdb = Parsed input sequences in fasta format, used for UPC generation etc. [[extras=0]{cmd:extras}]
masked = Masked input sequences (masked residues marked with X) [[extras=1]{cmd:extras}]
mapping = Fasta format with positions of SLiM occurrences aligned [[extras=1]{cmd:extras}]
motifaln = Fasta format of individual SLiM alignments (unmasked sequences) [[extras=1]{cmd:extras}]
maskaln = Fasta format of individual SLiM alignments (masked sequences) [[extras=1]{cmd:extras}]

Additional REST Outputs [extras>1]

To get additional REST outputs, set &extras=2 or &extras=3. This may increase run times noticeably,
depending on the number of SLiMs returned.

motifs = SLiM predictions reformatted in plain motif format for CompariMotif [[extras=2]{cmd:extras}]
compare = Results of all-by-all CompariMotif search of predicted SLiMs [[extras=2]{cmd:extras}]
xgmml = SLiMs, occurrences and motif relationships in a Cytoscape-compatible network [[extras=2]{cmd:extras}]
dismatrix = Input sequence distance matrix [[extras=3]{cmd:extras}]
rank = Main table in SLiMDisc output format [[extras=3]{cmd:extras}]
dat.rank = Occurrence table in SLiMDisc output format [[extras=3]{cmd:extras}]
teiresias = Motif prediction output in TEIRESIAS format [[extras=3]{cmd:extras} [teiresias=T]{cmd:teiresias}]
teiresias.fasta = TEIRESIAS masked fasta output [[extras=3]{cmd:extras} [teiresias=T]{cmd:teiresias}]