Web Tools

This selection of web tools are freely available and allow users to analyze sequences on the Web. Commercial software or applications which must be downloaded and used locally have not been included. Links added in the last update are marked - NEW. To suggest additional links or if you discover that a link is broken, please contact the Editorial Office.

These links are provided for the convenience of World Wide Web users. Cancer Immunity is not responsible for the availability or content of these external sites, nor does Cancer Immunity endorse, warrant or guarantee the products, services, or information described or offered at these other Internet sites.

Proteasomal Cleavage


PAProC – Prediction Algorithm for Proteasomal Cleavages
Department of Immunology and Department of Biomathematics, Eberhard-Karls-University Tübingen – Tübingen, Germany

NetChop – prediction of cleavage sites of the human proteasome
Center for Biological Sequence Analysis, Technical University of Denmark – Lyngby, Denmark

MAPPP – MHC-I Antigenic Peptide Processing Prediction (FragPredict)
Max Planck Institute for Infection Biology – Berlin, Germany

TAP Binding


TAPPred – prediction of TAP binding peptides
Bioinformatics Centre, Institute of Microbial Technology – Chandigarh, India

MHC-Peptide Binding


RankPep – prediction of MHC binding peptides
Molecular Immunology Foundation

MHCBench – benchmark MHC binding peptide prediction algorithms
Bioinformatics Centre, Institute of Microbial Technology – Chandigarh, India

HLA Peptide Binding Predictions (BIMAS) – prediction of binding affinities for HLA class I molecules
BioInformatics & Molecular Analysis Section, CBEL, CIT and NIH – Bethesda, MD

PREDEP – MHC Class I epitope prediction
Department of Molecular Genetics and Biotechnology, The Hebrew University of Jerusalem – Jerusalem, Israel

nHLAPred – MHC Class-I binding peptide prediction
Bioinformatics Centre, Institute of Microbial Technology – Chandigarh, India

ProPred-I – promiscuous MHC Class-I binding peptide prediction
Bioinformatics Centre, Institute of Microbial Technology – Chandigarh, India

SVMHC – prediction of MHC class I binding peptides
Stockholm Bioinformatics Center, Stockholm University – Sweden

EPIPREDICT – MHC class II binding peptide prediction
Institute of Immunology – Rikshospitalet, Oslo AND Dept. of Onkology/ Immunology, University Childrens Hospital – Tübingen, Germany

ProPred – prediction of HLA-DR binding sites
Bioinformatics Centre, Institute of Microbial Technology – Chandigarh, India

NetMHC – prediction of binding affinities for HLA-A2 and H-2Kk
Center for Biological Sequence Analysis, Technical University of Denmark – Lyngby, Denmark

NetMHCII – prediction of binding affinities for different HLA-DR
Center for Biological Sequence Analysis, Technical University of Denmark – Lyngby, Denmark

NetMHCpan – prediction of binding affinities for different HLA-A and -B
Center for Biological Sequence Analysis, Technical University of Denmark – Lyngby, Denmark

SMM – prediction of high affinity HLA-A2-binding peptides
Boston University – Boston, MA

POPI – prediction of immunogenicity of binding peptides of MHC class I and II
Institute of Bioinformatics, National Chiao Tung University – Hsin-Chu, Taiwan

OptiTope – determination of an optimal set of epitopes with respect to overall immunogenicity in a specific individual or a target population
Division for Simulation of Biological Systems, University of Tübingen – Tübingen, Germany

Mosaic Vaccine Tool Suite – design and assess vaccine candidate protein sequences
Los Alamos National Laboratory – Los Alamos, NM

HLABinding – prediction of MHC class I binding peptides
Microsoft Research – Redmond WA

Antigenic Peptides


Prediction of Antigenic Determinants – prediction of peptides likely to elicit an antibody response
Molecular Immunology Foundation
Additional information here

ANTIGENIC (EMBOSS package) – prediction of peptides likely to elicit an antibody response
Institut Pasteur – Paris, France
Search for “antigenic”

BepiPred – prediction of linear B-cell epitopes
Center for Biological Sequence Analysis, Technical University of Denmark – Lyngby, Denmark

DiscoTope – prediction of discontinuous B-cell epitopes
Center for Biological Sequence Analysis, Technical University of Denmark – Lyngby, Denmark

ElliPro – prediction of peptides likely to elicit an antibody response
National Institute of Allergy & Infectious Diseases – Bethesda, MD

Antibody Epitope Prediction – prediction of continuous linear B cell epitopes
National Institute of Allergy & Infectious Diseases – Bethesda, MD

CTL Epitopes


CTLPred – prediction of CTL epitopes
Bioinformatics Centre, Institute of Microbial Technology – Chandigarh, India

NetCTL – prediction of CTL epitopes
Center for Biological Sequence Analysis, Technical University of Denmark – Lyngby, Denmark

MHC-I processing predictions – prediction of a peptide’s intrinsic potential of being a T cell epitope
National Institute of Allergy & Infectious Diseases – Bethesda, MD

Epitope Analysis


Epitope Cluster Analysis – grouping of epitopes into clusters based on sequence identity
National Institute of Allergy & Infectious Diseases – Bethesda, MD

Epitope Conservancy Analysis – determination of the fraction of protein sequences containing an epitope at a given identity level
National Institute of Allergy & Infectious Diseases – Bethesda, MD

Tumor Antigens


VaxiJen – prediction of tumor antigens
Edward Jenner Institute for Vaccine Research – United Kingdom