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FRED / FRamework for Epitope Detection

A versatile immunoinformatics software framework enabling a unified interface to many tools, from epitope prediction, HLA typing, to epitope selection and assembly. Its openness and easy extensibility makes FRED 2 a perfect instrument for the development of advanced immunoinformatics pipelines that are needed for example in cancer immunotherapy development and other areas of personalized medicine. By building on top of popular modules such as BioPython and Pandas, FRED 2 allows rapid prototyping of complex and innovative immunoinformatics applications.

EpiToolKit

A virtual workbench for immunological questions with a focus on vaccine design. EpiToolKit offers an array of immunoinformatics tools covering MHC genotyping, epitope and neo-epitope prediction, epitope selection for vaccine design, and epitope assembly. In its recently re-implemented version 2.0, EpiToolKit provides a range of new functionality and for the first time allows combining tools into complex workflows. For inexperienced users it offers simplified interfaces to guide the users through the analysis of complex immunological data sets.

ImmunoNodes

Permits to build complex workflows. ImmunoNodes is integrated in KNIME that provides a way to predict Human Leukocyte Antigen (HLA) binding, HLA class I antigen processing, HLA genotyping, as well as epitope-based vaccine design including epitope-selection and string-of-beads assembly. It allows users to develop complex analysis workflows without the need of having mastered a programming language. The tool offers the possibility to diffuse the usage of state-of-the-art immuno-informatics methods.

PolyCTLDesigner

A program that is intended for constructing polyepitope immunogens. Given a set of either known or predicted T-cell epitopes the program selects N-terminal flanking sequences for each epitope to optimize its binding to TAP (if necessary) and joins resulting oligopeptides into a polyepitope in a way providing efficient liberation of potential epitopes by proteasomal and/or immunoproteasomal processing. And it also tries to minimize the number of non-target junctional epitopes resulting from artificial juxtaposition of target epitopes within the polyepitope. For constructing polyepitopes, PolyCTLDesigner utilizes known amino acid patterns of TAP-binding and proteasomal/immunoproteasomal cleavage specificity together with genetic algorithm and graph theory approaches.

Create Epitome

Obsolete
Models genetic diversity by summarizing a large input dataset into an epitome, a short sequence capturing many overlapping subsequences from the dataset. Create Epitome is an interactive program (created via Silverlight) and a command-line program for Windows. Given a weighted set of amino-acid sequences, it creates a new amino-acid sequence that covers input sequences. It works step-by-step, producing an output line after each step. The possible steps include: combining two input sequences that overlap, adding an input sequence to an output component with which it overlap, combining two output components that overlap.