Algorithms in Bioinformatics - #27623

LITERATURE:

Online material (This list will be updated on a regular basis to include additional material relevant for the different topics in the course). The password to the projected files will be provided in the first lecture of the course (Tuesday 30th of August, 2011).

C-programming

• Notes on C-programming

PSSM

• Immunological Bioinformatics. MIT Press. Chapter 3.
• Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Altschul SF et al. Nucleic Acids Res. 1997 Sep 1;25(17):3389-402.

Alignment

• Immunological Bioinformatics. MIT Press. Chapter 3.
• A General method applicable to search for simularities in the amino acid sequences of two proteins. S. B. Needleman and C. D Wunsch J.Mol. Biol (1970), 48.
• Identification of common molecular subsequences. T. F. Smith and M. S. Waterman. J. Mol. Biol. (1981), 147.
• An improved algorithm for matching biological sequences. O. Gotoh. J. Mol. Biol. (1982), 162.

Gibbs sampling

• Improved prediction of MHC class I and class II epitopes using a novel Gibbs sampling approach.Bioinformatics. 2004 Jun 12;20(9):1388-97.
• Simultaneous alignment and clustering of peptide data using a Gibbs sampling approach.Bioinformatics. 2012 Oct 24. [Epub ahead of print]

Hobohm

• Lund 1997
• Hoborm 1992

HMM

• Krogh 1998
• Eddy 2004

Support vector machines

• Ivancius 2007
• Quyuan 2007
• Burges 1998 (tutorial on SVM)
• Keerthi 2001

MIT Press

• Lund et al. MIT Press 2005, chapters 3 and 4