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SLiMProb

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Emily Saunders Walmsley edited this page Jun 3, 2015 · 4 revisions

##SLiMProb

SLiMProb Input tree; follow any one branch.

SLiMProb searches the protein sequences of the selected nodes for occurrences of a specified regular expressions; useful for locating new instances of a motif found using SLiMFinder (e.g. R[SFYW].S.P). Conventions as used in the program can be found here.

SLiMProb has one input; a SLiM to be searched for in the nodes selected on the graph. To run SLiMProb you must provide a regular expressions in the motifs box and select one or more nodes. Alternatively, if you know the run ID of a previous search, you can instead input that to the Run ID textbox.

If the motif is found, the colour and shape of the target node will change.

###SLiMProb 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.

Custom Parameters

  • Custom parameters can be used to add other command line arguments which can be found here.

##Results Results for SLiMProb are displayed in two panels.

Main Results Panel contains:

  • Motif: The name of the motif.
  • Pattern: The motif definition.
  • IC: Information content.
  • N_Occ: Number of specified SLiM occurrences.
  • N_Seq: Number of nodes the SLiM occurred in.
  • N_Upc: Number of nodes in the unrelated protein cluster (UPC).
  • E_Upc: Enrichment score for the unrelated protein cluster.
  • p_Upc: Significance value of the unrelated protein cluster.
  • pUnd_Upc: Probability of seeing the observed number of occurrences or less of the UPC.

OCC Panel contains:

  • Motif: The motif found in the sequence.
  • Seq: The name of the sequence.
  • Start_Pos: The start position of the sequence.
  • End_Pos: The end position of the sequence.

The nodes in the graph that contain SLiMs will change, becoming red diamonds. Nodes with multiple SLiMs will be a darker shade of red.

###Sample Output Sample SLiMProb output, given the input motif of L.C.E

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