Bioinformatics Interest Group (BIG) at Waikato University

This is the interim homepage for the Bioinformatics Interest Group.

People

• People involved in the interest group

Graduate module

• COMP555 2017

peptide-MHC affinity prediction

• quick-start overview from MIF.
• paper on SVM and HMM approach to MHC class II prediction.
• some papers on peptide-MHC affinity predicition from the National Bioinformatics Center in Cuba.
• a paper on "Improved prediction of MHC class I and class II epitopes using a novel Gibbs sampling approach": Morten Nielsen, Claus Lundegaard, Peder Worning, Christina Sylvester Hvid, Kasper Lamberth, Soren Buus, Soren Brunak, and Ole Lund Bioinformatics 2004 20: 1388-1397.
  
  
• MHC data (most of which has been provided by Victor at BioInfo)
  • training data (arff) for peptide-MHC problem
  • test data (arff) for peptide-MHC problem
  • combined training and test data (from above) in plaintext -- first field is 1 (binding) or 2 (nonbinding) and second field is the peptide
  • allele HLA_A2 (MHC class I) binding and non-binding length 9 peptides from MHCBN database
  • Some notes on the peptide-MHC affinity data.
  • CVS formatted properties of amino acids
  • basic question about MHC/HLA and antibodies

Amino Acids

• imb-JENA properties of amino acids
• properties of amino acids
• basic chemistry of amino acids

Seminars, Talks and Projects in Bioinformatics

• Talk for Bioinformatics Congress (Havana, 2004)
• ACM (student chapter) bioinformatics presentation
• Info Day bioinformatics presentation
• PacRim 2002 invited presentation
• Summer Research Work in Computational Biology
• 2004 Honours project B (Machine Learning from microarray data)
• SIG.red protein cleavage site data
• description of the SIG.red protein cleavage data