RAPTOR GUI

Welcome to the RAPTOR GUI page. This page has been developed for those interested in seeing what RAPTOR has to offer, but without having to install the software for a demo evaluation.

If you care to read more about fold recognition, check out our Fold Recognition/Protein Threading Basics page.

Create a Project

The RAPTOR software is streamlined for user ease. We will start by creating a new project and loading in a sample sequence. To create a new project, click “File” in the menu and select “New -> New Project”.

The "New Project" dialog appears where you have to provide a project name, which will generate a project file. Take this time to provide a location where to save the project file and also a location for the project output folder.

After providing this information, click the “Create” button to create a new empty project. In the “Project Properties” window, the properties of the current project will be displayed. To use RAPTOR, you have to add a sequence to the project.

Load a Sequence

To load a sequence (in FASTA format), right click on the project node in the project tree. A popup menu will appear. Select command “Add Sequence (FASTA) File”. In the open sequence dialog, you can browse to RAPTOR\data\sample\ directory and load one sample sequence into the project.

After that, the sequence will be displayed as a sequence node under the project node in the project tree on the left panel and the content of the sequence will be displayed in a window on the right.

Run a Sequence

To run the selected sequence, click “Run” in the menu and select “Run Blast” or “Run Raptor” as shown below. Basically, PSI-Blast can be run first. If it cannot find a significant match, then try RAPTOR threading.

After you select “Run Blast”, a configuration panel pops up.
The default parameters are provided. Click “Run” to start PSI-BLAST. PSI-BLAST first searches NR (non-redundant) database to generate the sequence profile. Then it searches against sequences whose structures are stored in PDB. You can also specify your sequence library for each step if applicable. After PSI-BLAST search, 3D modeling module OWL is called to build 3D structures from the alignments.

After you select “Run Raptor”, a configuration panel pops up as displayed below. The default parameters are provided. Click “Run” to start RAPTOR. There are three threading engines available. By default, “NP Core” is used. After threading, 3D modeling module “OWL” is used to build 3D models.

For the test purpose, just click “Run” and RAPTOR will start to run. It will take about one hour for RAPTOR to run one sequence, depending on the sequence length. PSI-BLAST is much faster and will take about 10 minutes to finish one sequence. After the sequence is finished, all the outputs will be added to the project and the project will be updated. You will find PSP matrix obtained by PSI-BLAST, predicted secondary structure, ranking list of templates, all the alignments and PSI-BLAST output.

Load Sample Project

You can find a sample project file “test_raptor_project.xml” and its output folder “test_raptor_project” in the folder “%RAPTOR_HOME%\data\sample”. From “File” menu, select the command “File->Open->Open Project” and a file browser will appear. Select the project file “%RAPTOR_HOME%\data\sample\test_raptor_project.xml”. The project file will be loaded into RAPTOR as shown here.

If you have any problem in loading the sample project or encounter any error message, then open the project file “test_raptor_prject.xml” in any text editor and check the nodes “” and “”. Make sure that this two entries are correct according to the settings in you computer.

This page was designed to simply give users and potential users a quick impression of what RAPTOR is capable of producing. Other features not discussed on this page, but possible with RAPTOR include; running multiple sequences, advanced configuration and simple navigation to relevant sequences within the NCBI website, just to name a few.