Cancer Vaccine Center

Bioinformatics Tools

The Bioinformatic Core supports vaccine development by combining information science, biostatistics, simulation and modeling techniques. We perform vaccine research in silico and provide informatics and statistical support for the design and analysis of laboratory experimentation in the CVC. Bioinformatic tools and resources developed at CVC and some of the popular solutions are accessible through our server.

Databases

TANTIGEN
Data source and analysis platform for cancer vaccine target discovery focusing on human tumor antigens that contain HLA ligands and T cell epitopes

DFRMLI
This repository contains lists of MHC-binding peptides and T-cell epitopes that could be used to develop machine learning methods for immunology.

Tools

Immunology

RANKPEP
Predicion of MHC binding peptides from an input protein using Position Specific Scoring Matrixes (PSSM). Reche et al,. 2004 [PMID: 15349703]

PEPVAC
Multi-epitope Vaccine Design A tool for the development of MHCI-restricted multi-epitope vaccines.Reche and Reinherz, 2005 [PMID: 15980443]

Sequence Analysis and Manipulation

Dachisi
Prediction and classification of histones using SVM.

Methylator
Predicts methylation of cythosines from a DNA sequence.

Structure Analysis

SVA
Sequence variability and consensus plots
Variability plots from multiple sequence alignments using Shannon entropy.

H2PDB
Map Sequence variability (H) onto a 3D structure

Solvent Accessibility Tool
Identifyisolvent exposed hydrophobic residues within a protein sequence, and compares them with those of closely related sequences.