– Motifs are specified in SMART format (
– A motif is described by a single tab delimited line of amino acids.
– Default definition of a motif is given by a single letter, however multi-letter motifs can be specified.
– To add a motif to the motifs panel, you need to double click on the panel, select the motif and the panel will display the motif structure.
– To save the SLiM discovered within the current panel, you need to select the Apply button.
– To keep track of the number of motifs detected and the count of occurrences within each motif the panel displays a counter
– Additional panels are opened if nested networks or nodes are selected
– A log window is available for each panel and can be accessed with the Log button in the SLiMScape menu
– Graphical output can be saved and loaded to disk using the export buttons located in the bottom right of the panel.
– Graphical results can be shown in Cytoscape format using the view.graph() Cytoscape method
– Graphical results can be saved to disk for subsequent retrieval using the export_graph.html method
– The plugin is interactive and can handle up to 128 motifs in parallel
– You can click on any node in the network to launch the motif detector and a window will appear at the top right corner of your screen, providing you with a list of all motifs discovered. You will also see a log message indicating the number of motifs found. A screenshot of the panel can be found in the tutorial video at

SLiMScape for Cytoscape perfectly integrates within Cytoscape and enables you to easily transform DNA motif analysis into a SLiM discovery platform.
Analysis panels are initially empty and are populated each time you run a set of nodes or nested networks using SLiMFinder or SLiMSearch.
The plugin provides you with a user-friendly interface and helps you identify new instances of a predefined motif in the protein interaction network.
KEYMACRO Description:
– Motifs are specified in SMART format (
– A motif is described by a single tab delim 384a16bd22

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– Alpha mod (Alt+G): Activate the use of Grayscale mod (Alt+G)
– Channel: Activate the use of RGB mode
– Clip: Activate the use of Clip mode
– Convolve: Activate the use of Convolution mod
– Contrast: Activate the use of Contrast mod
– Gamma: Activate the use of Gamma mod
– Hardlight: Activate the use of Hardlight mod
– Lighten: Activate the use of Lighten mod
– Vibrance: Activate the use of Vibrance mod
– Vignette: Activate the use of Vignette mod
– Hue: Activate the use of Hue mod
– Channel Mix: Activate the use of Channel Mix mod
– Grain: Activate the use of Grain mod
– Cutoff: Activate the use of Cutoff mod
– HSV Saturation: Activate the use of Saturation mod
– HSV Value: Activate the use of Value mod
– Chroma key (CC) only in Supertweak Channel Mix and Saturation: Activate the use of Chroma Key (CC) mod
– Chroma key (CC) only in Supertweak Mix and Vibrance: Activate the use of Chroma Key (CC) mod
– Chroma key (CC) in Supertweak only: Activate the use of Chroma Key (CC) mod
– Channel Mix: Activate the use of Channel Mix mod
– Color boost: Activate the use of Color boost mod
– Color Correction: Activate the use of Color Correction mod
– Luma key (Y): Activate the use of Luma Key mod
– Luminance: Activate the use of Luminance mod
– Black: Activate the use of Black mod
– White: Activate the use of White mod
– Chroma Key (CC): Activate the use of Chroma Key mod
– White Balance: Activate the use of White Balance mod
– Emphasis: Activate the use of Emphasis mod
– Colorize: Activate the use of Colorize mod
– Chroma key (CC) white balance only: Activate the use of White balance mod
– Chroma key (CC) white balance only: Activate the use of White balance mod
– Auto: Activate the use of Auto mod
– Auto White Balance: Activate the use of Auto White Balance mod
– Auto Contrast: Activate the use of Auto Contrast mod
– Auto Lighting: Activate the use of Auto Lighting mod
– auto (any): Activate the use of

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