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SLiMFinder

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Emily Saunders Walmsley edited this page Jun 3, 2015 · 5 revisions

##SLiMFinder

SLiMFinder Inputs Tree: follow any one branch. SLiMFinder aims to discover new motifs in the selected protein interaction network by searching for statistically overrepresented sequences within a set of proteins.

It has no mandatory inputs other than a selection of graph nodes or a run ID. If a motif is found in a node, the node will change colour and shape. The specific motif is presented in an output table, along with the Uniprot ID and other data.

###SLiMFinder Options

Masking

  • Disorder Masking is used to mask residues which have an IUPred disorder score of less than 0.3
  • Conservation Masking is used to mask residues which have a relative local conservation score of less than X.
  • Feature Masking is used to mask residues which occur in features such as domains or transmembrane regions.

SLiMChance

  • Probability Cutoff is the cutoff for returned motifs.

Miscellaneous Options

  • Walltime is the maximum runtime of a single run.
  • Custom parameters is used to add other command line arguments which can be found here.

###Results

Results for SLiMFinder are displayed in two panels:

Main Results Panel contains:

  • Rank: Rank of the motifs found, from most to least common.
  • Sig: Motif significance value.
  • Pattern: Regex of the motif found.
  • IC: Information content of the motif.
  • OCC: Enrichment score for the occurence(s).
  • Support: Number of sequences the motif occurs in (no distinction made between motifs with multiple occurences).
  • UP: Unrelated proteins the motif occurs in.z

OCC Panel contains:

  • Pattern: Regex of the motif found.
  • Sig: Motif significance value.
  • Seq: The name of the sequence.
  • Start_Pos: The start position of the sequence.

On the graph, nodes possessing SLiMs will become red diamonds. If multiple SLiMs are present in a single node, that node will be a darker shade of red.

Further results can be obtained on the internet, at the URL: http://rest.slimsuite.unsw.edu.au/retrieve&jobid={jobid produced when the run is performed}. Alternatively, there is a button at the bottom of the results panel which will open the above link in your browser.

###Sample Output: Sample Output

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