The tools below are
intended for the
detailed analysis
of a known epitope sequence or group of sequences.
- Population
Coverage
- 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.
- Epitope
Conservancy Analysis
- 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.
- Epitope
Cluster
Analysis
- 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.
- Homology
Mapping
- This tool maps linear and conformational epitopes
to 3D structures of
proteins.
This is done by comparing the epitope source protein sequence with that
of proteins with known 3D structures in the PDB. The tool generates an
alignment between the query sequence of the epitope source sequence and
a homologous sequence from the PDB, and allows to visualize the result
in an EpitopeViewer.
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