Analysis ToolsThe tools below are intended for the detailed analysis of a known epitope sequence or group of sequences.
This tool calculates the fraction of individuals predicted to respond to a given set of epitopes with known MHC restrictions. This calculation is made on the basis of HLA genotypic frequencies assuming non-linkage disequilibrium between HLA loci.
This tool calculates the degree of conservancy of an epitope within a given protein sequence set at different degrees of sequence identity. The degree of conservation is defined as the fraction of protein sequences containing the epitope at a given identity level.
This tool groups epitopes into clusters based on sequence identity. A cluster is defined as a group of sequences which have a sequence similarity greater than the minimum sequence identity threshold specified.
This page provides information on available methods for mimotope mapping, how to search the IEDB for mimotopes, and an example of a mimotope dataset and the results of its mapping, using the available web servers hosted outside the IEDB.
The RATE is an automated method that can infer HLA restriction for a set of given epitopes from large datasets of T cell responses in HLA typed subjects. The tool takes two data files, one containing the alleles expressed by the subjects and the other containing the response of the peptides in the subjects. The tool calculates the odds ratio and estimates its significance using Fisher's exact test. It also calculates a parameter called relative frequency similar to odds ratio. The tool was developed with a focus on class II alleles but can also be applied to class I alleles.
This tool groups epitopes into clusters based on sequence identity. A cluster is defined as a group of sequences which have a sequence similarity greater than the minimum sequence identity threshold specified. User can also select the minimum and maximum length of peptide and also one of the three approaches for clustering of peptides.
The tool is helpful to aggregate and visualize immune reactivity from epitope data in different assays/donors in given reference proteins using user-defined identity thresholds. The tool also accepts predicted epitopes.
Coming soon: DockTope webserver was proposed by Rigo et al.
: Tools under AR Labs which are experimental and are not quite ready for production yet. They are intended for further research, updates and testing.