REMUS: a tool for identification of unique peptide segments as epitopes

Abstract

We provide a ‘R E MUS’ (reinforced merging techniques for unique peptide segments) web server for identification of the locations and compositions of unique peptide segments from a set of protein family sequences. Different levels of uniqueness are determined according to substitutional relationship in the amino acids, frequency of appearance and biological properties such as priority for serving as candidates for epitopes where antibodies recognize. R E MUS also provides interactive visualization of 3D structures for allocation and comparison of the identified unique peptide segments. Accuracy of the algorithm was found to be 70% in terms of mapping a unique peptide segment as an epitope. The R E MUS web server is available at http://biotools.cs.ntou.edu.tw/REMUS and the PC version software can be freely downloaded either at http://bioinfo.life.nthu.edu.tw/REMUS or http://spider.cs.ntou.edu.tw/BioTools/REMUS . User guide and working examples for PC version are available at http://spider.cs.ntou.edu.tw/BioTools/REMUS-DOCS.html , and details of the proposed algorithm can be referred to the documents as described previously [H. T. Chang, T. W. Pai, T. C. Fan, B. H. Su, P. C. Wu, C. Y. Tang, C. T. Chang, S. H. Liu and M. D. T. Chang (2006) BMC Bioinformatics , 7 , 38 and T. W. Pai, B. H. Su, P. C. Wu, M. D. T. Chang, H. T. Chang, T. C. Fan and S. H. Liu (2006) J. Bioinform. Comput. Biol ., 4 , 75–92].