SLiMScape is a visualisation and discovery platform for sequence-based motifs from the TRANSFAC database. Currently supports motifs from the following species: - Human - Mouse - Rat - Dog - Chicken - Xenopus - Zebrafish - Tetraodon The plugin currently enables you to: - Identify motif instances in protein interactions - View selected motif instances in the interaction network - View motif instances in 3-D - Visualise instances of the motif in a pre-computed protein interaction network - Integrate information about motif instances into the network - Find motif instances in additional networks - Find motif instances in other databases - Find motif instances from other species - Save and load profiles The Cytoscape UI is simple and intuitive. Features: - Full integration with the Cytoscape API - Maintains current state of the motif instances and network in the interaction profile - Visualisation panel which shows the motif instance in context of the network, updated with every interaction - Preview pane which shows an animated view of the network, with the motif instance at the centre - SLiMFinder panel, which lets you search for a motif instance in the network - SLiMSearch panel, which allows you to query a motif in the network - Saving and loading of protein interaction networks - The ability to export the current motif instances to the TRANSFAC database for batch processing - The ability to build motifs - A wide range of profile types - The ability to build profiles in parallel, in a scheduled mode, or in real-time - The ability to save and load profiles - The ability to build motifs from a database of pre-defined motifs - The ability to select multiple motif instances in the network and to search for those instances - The ability to find motif instances in a single network, and to find motif instances in additional networks - The ability to search multiple motif instances in the network, and to find motif instances in additional networks - The ability to query motif instances from other species - The ability to query motif instances in a database - The ability to query motif instances from a user-defined database - The ability to apply to multiple queries (find motif instances in different species, in different databases) - The ability to export to the database - The ability to export to the database in batch - The ability to run user
SLiMScape for Cytoscape Crack Mac is a Cytoscape plugin that enables you to upload a set of interaction networks for motif discovery. The plugin displays the motifs on the nodes and edges of the network. It automatically detects the selected motif and provides information on the occurrence of the motif on the nodes and edges of the networks. Features: Analyze and visualize protein interaction networks Analyze proteins Search for motifs in networks Analyze proteins with motifs Contact: Johan Van Iersel, EFI (Competence Center Cytoscape, Evry) [email protected] Phone: Email: Website: Version: Tags: 972550f159
- 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
OS: Windows 7/8/10 (64-bit), Windows Vista (32-bit) Processor: Intel Core i3, Core i5, Core i7 (Xeon or Core 2 Duo), AMD Athlon or AMD Sempron Memory: 4 GB RAM Hard Disk Space: 25 GB available space Graphics Card: Intel HD Graphics 3000, AMD HD 8000/HD 9000 or Nvidia Geforce 450 DirectX: Version 11 Network: Broadband Internet connection Other: Anti-virus software (A
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