- #SEARCHGUI REFERENCE ZIP FILE#
- #SEARCHGUI REFERENCE FULL SIZE#
- #SEARCHGUI REFERENCE MANUAL#
- #SEARCHGUI REFERENCE DOWNLOAD#
The simplest way to make your own configuration file is to select the wanted settings in the GUI version of SearchGUI and save these to a file using the "Save" option in the user interface.SearchCLI SearchGUI Command Line Interface Note that the automatic check for newer versions of SearchGUI will not be performed when running in command line mode. Any output from the tool or the search engines will be displayed in the command line window. An example command line: java -cp SearchGUI-X.Y.Z.jar eu. -no_gui -search -omssa -xtandem -cf my_config_file -rf my_results_folder -sf my_spectrum_folderThis will start SearchGUI and run the search, but no GUI will be displayed. To start SearchGUI from the command line use the following command: java -cp SearchGUI-X.Y.Z eu. available options and inputs: -no_gui : hides the graphical user interface -search : starts the search automatically -omssa : enables OMSSA search -xtandem : enables XTandem search -cf config_file : the configuration file -rf results_folder : the results folder -sf spectra_file_1 : the spectra files, either as files or folders To show the usage description in the command line use the -h (or -help or -usage) option. With this in mind we have therefore included the option of using SearchGUI as a command line tool. For example when incorporating the search into some sort of pipeline. However, it can sometimes be easier to perform a search from the command line. We believe that a graphical user interface would be the best choice for most users, and therefore made SearchGUI with a graphical user interface. Below is an example of how this can be achieved: // set the parent frame of SearchGUI JFrame parentFrame = "your parent frame" // set the location of the configuration file to use File configFile = new File("location of your configuration file") // set the location of the results folder to use File resultsFolder = new File("location of your results folder") // create a list of the spectra files to use in the search ArrayList spectraFiles = new ArrayList () // add the spectra files to the list spectraFiles.add(new File("spectrumFileA.mgf")) spectraFiles.add(new File("spectrumFileB.mgf")) // open a new SearchGUI with all parameters already filled in SearchGUI searchGUI = new SearchGUI( parentFrame, configFile, resultsFolder, spectraFiles) Go to top of page From the Command LineThe main purpose of SearchGUI is to make it simpler to use multiple search engines at the same time. Go to top of page In Other ToolsIt is easy to use SearchGUI in other Java tools.
#SEARCHGUI REFERENCE MANUAL#
For additional help see the SearchGUI manual which is also found in the downloads section.
#SEARCHGUI REFERENCE DOWNLOAD#
Go to top of page Using SearchGUITo start identifying peptides and proteins using SearchGUI, download the latest version in the downloads section, unzip the downloaded file, and double-click on the SearchGUI-X.Y.Z.jar file. In the downloads section you will also find the SearchGUI manual.
#SEARCHGUI REFERENCE ZIP FILE#
Go to top of page DownloadThe zip file in the downloads section contains the SearchGUI jar file and all the libraries needed to run the tool. With help from Lennart Martens and Harald Barsnes. The main part of the additions have implemented by Marc Vaudel from ISAS, Germany. SearchGUI is based on the OMSSAGUI project. What is SearchGUI?SearchGUI is a user-friendly, lightweight and open-source graphical user interface for configuring and running two proteomics identification search engines simultaneously, namely the Open Mass Spectrometry Search Algorithm (OMSSA) and X!Tandem. See ReleaseNotes for complete list of changes. Simplified the folder structure in the zip file. 2012: SearchGUI v1.8.3 is now available: Made it possible to cancel the reading of FASTA sequences and the adding of decoy sequences. Re-added the config settings to the Search tab. 2012: SearchGUI v1.8.4 is now available: Fixed an issue with some missing icons in the PtmDialog resulting in an error opening the dialog. Displays in the search tab whether a file has been loaded or user settings used. 2012: SearchGUI v1.8.5 is now available: SearchGUI will not complain about the settings if a parameter file is loaded.
#SEARCHGUI REFERENCE FULL SIZE#
(Click on figure to see the full size version) NewsMay 10. OMMSA Parser and X!Tandem Parser: For developer access to the search results we recommend the use of OMSSA Parser and XTandem Parser. PeptideShaker: To visualize and analyze the search results we recommend the use of PeptideShaker. If you use SearchGUI as part of a paper, please include the reference above. SearchGUINews What is SearchGUI? Download Using SearchGUI In Other Tools From the Command Line Database Help User Defined Modifications Result Analysis Troubleshooting SearchGUI Publication: Vaudel et al: Proteomics 2011 11(5):996-9.
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