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BepiPred 1.0 Server

BepiPred 1.0 server predicts the location of linear B-cell epitopes using a combination of a hidden Markov model and a propensity scale method.

Instructions Output format Data sets Article abstract


Paste a single sequence or several sequences in FASTA format into the field below:

Submit a file in FASTA format directly from your local disk:

Score threshold for epitope assignment        

At most 2000 sequences and 200,000 amino acids per submission; each sequence not less than 10 and not more than 6000 amino acids.

The sequences are kept confidential and will be deleted after processing.


For publication of results, please cite:

Improved method for predicting linear B-cell epitopes
Jens Erik Pontoppidan Larsen, Ole Lund and Morten Nielsen
Immunome Research 2:2, 2006.

View the abstract.


Would you prefer to run BepiPred at your own site? BepiPred 1.0 is available as a stand-alone software package, with the same functionality as the service above. Ready-to-ship packages exist for the most common UNIX platforms. There is a download page for academic users; other users are requested to contact CBS Software Package Manager at


Scientific problems:        Technical problems: