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

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REMUS a tool for identification of unique
peptide segments as epitopes

• Dr. Tun-Wen Pai
• Dept. of Computer Science and Engineering,
  National Taiwan Ocean University
• 2006/10/30

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• REMUS A web server for identification of the
  locations and compositions of unique peptide
  segments from a set of protein family sequences (
  http//140.121.196.30/remus)
• DNA / PROTEIN levels
• Web interface / PC version for Windows
• Refs
• 1. H. Chang, T. Pai, D. Chang, et al., A
  Reinforced Merging Methodology for Mapping
  Unique Peptide Motifs in Members of Protein
  Families, BMC Bioinformatics 738 (SCI), 2006.
• 2. T. Pai, M. Chang, W. Tzou, et al., REMUS a
  tool for identification of nique peptide
  segments as epitopes, Nucl. Acids Res. Web
  Server Issue(in press) (SCI) , 2006.

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System Architechure
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• System features
• Bottom-up approximate searching technology
• Statistical properties analysis for each primary
  
• segment (Uniqueness Representation)
• Automatic / Semi-Automatic version
• (Automatic Primary Pattern Analysis)
• Substitutable Residues (BLOSUM/PAM)
• Various Merging Methods
• Chemical Properties (Ranking Order)
• Structural Representation
• (loop structure analysis)

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Example (Web Version)
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Example (Results of REMUS)
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Example (3D representation)
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Example (UPM representation)
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Example (Various Styles)
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• LEPD (Linear Epitope Prediction Database)
• Designed for identification of unique peptide
  motifs (UPMs)
• as specific linear epitopes from all family
  protein sequences
• UPMs in each protein family searched by updated
  the Pfam
• database (http//www.sanger.ac.uk/Software/Pfa
  m/)
• Identification of the potential linear epitopes
  with different
• levels of antigenicities
• Three-dimensional structure display and
  Conformational
• Epitope Prediction

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