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

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

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

Flavivirus Antigen Database
A data mining system for knowledge discovery in flaviviruses with direct applications in immunology and vaccinology.

FluKB
A knowledge-based system for evaluation and assesment of influenza vaccine target discovery.

Epstein-Barr Virus T cell Antigen Database
Data source and analysis platform for EBV immune target discovery by focusing on EBV antigens that contain HLA ligands and T cell epitopes.

Human Papillomavirus T cell Antigen Database
Data source and analysis platform for HPV immune target discovery by focusing on HPV antigens that contain HLA ligands and T cell epitopes.

Tools

Immunology

MULTIPRED2
Large-scale screening of peptide binding to multiple alleles belonging to human leukocyte antigen (HLA) class I and class II DR supertypes as well as to alleles belonging to an individual's genotype. Zhang et al,. 2010 [PMID: 21130094]

PREDmafa
In silico identification of peptides binding to MHC alleles of cynomolgus macaques.

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

BlockLogo
Sequence logo visualization of peptide and sequence motif conservation.

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.

HLAV3D
Create a three dimensional representation of variability in HLA molecules

Microarray Data Analysis

ProtMAT
An online webtool which implements the Concentration Dependent Analysis (CDA) algorithm for high density protein microarrays [PMID: 18393456]. It reads data files from in the Prospector output format and performs differential expression analysis.

 

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