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Nucleic Acids Research 2006 34(Web Server issue):W198-W201; doi:10.1093/nar/gkl188
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© The Author 2006. Published by Oxford University Press. All rights reserved
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Article

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

Tun-Wen Pai*, Margaret Dah-Tsyr Chang1,*, Wen-Shyong Tzou2, Bo-Han Su, Pei-Chih Wu, Hao-Teng Chang1 and Wei-I Chou1

Department of Computer Science and Engineering, National Taiwan Ocean University Keelung, Taiwan, Republic of China 1 Department of Life Science, Institute of Molecular and Cellular Biology, National Tsing Hua University Hsinchu, Taiwan, Republic of China 2 Institute of Bioscience and BioTechnology, National Taiwan Ocean University Keelung, Taiwan, Republic of China

*To whom correspondence should be addressed. Tel: +886 2 24622192, ext. 6618; Fax: +886 2 24623249; Email: twp{at}mail.ntou.edu.tw

*Correspondence may also be addressed to Margaret Dah-Tsyr Chang. Tel: +886 3 5742767; Fax: +886 3 5715934; Email: dtchang{at}life.nthu.edu.tw

Received February 14, 2006. Revised March 20, 2006. Accepted March 20, 2006.

We provide a ‘REMUS’ (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. REMUS 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 REMUS 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].

The authors wish it to be known that, in their opinion, the first two authors should be regarded as joint First Authors


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