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FRED

A Framework for T-cell Epitope Detection

FRED is a framework for T-cell epitope detection that offers consistent, easy, and simultaneous access to well established prediction methods for MHC binding and antigen processing. FRED can handle polymorphic proteins and offers analysis tools to combine, benchmark, or compare different methods. It is implemented in Python in a modular way and can easily be extended by user defined methods.

For question, comments, or suggestions please contact Magdalena Feldhahn.

Download

Download FRED Version 1.0. FRED is published under the GNU Lesser General Public License

Installation

Installation instructions can be found in the README.txt included with the FRED package. FRED was tested on Linux and MacOS.

The Python code of FRED is platform-independent and does not require a particular operating system, although it has been developed mostly on Linux. We have also successfully installed FRED on other Unix-derived platforms, e.g. MacOS X, and on Windows using cygwin.

Tutorial Documentation

A tutorial how to use FRED and the documentation of the API is available here as pdf. The documentation is also available in an html version in an zip archive.

Examples

Some basic examples for the usage of FRED along with all input data required are included with the FRED package (FRED/examples).

A short description of the examples included in the FRED package can be found here.

Citation

Feldhahn, M, Dönnes, P, Thiel, P, and Kohlbacher, O (2009).

FRED - A Framework for T-cell Epitope Detection

Bioinformatics, 25(20):2758-9.

EpiToolKit

EpiToolKit is a web server that provides simultaneous access to different MHC binding prediction methods. EpiToolKit also provides predictions of minor histocompatibility complex antigens (mHags). EpiToolKit is based on FRED.