BIO650 - Special topics in Bioinformatics - Spring Semester 2009-2010, 2010-2011

• Lecture slides (Protein structure prediction) [Download]
• Lecture slides (Sequence models) [Download]
• Lecture slides (Biological networks)[Download]
• Notes on multiple sequence alignment [Download]
• An example amino acid sequence fasta sequence

• Lecture slides (Protein structure classification) [Download]

• Lecture slides (Composition bias) [Download]
• Lecture slides (Multiple sequence alignment) [Download]
• Lecture slides (Introduction to protein structure) [Download]

• Lecture slides (Lecture 6-7 -in greek) [Download]
• Lecture slides (Lecture 8-9 -in greek) [Download]
• Paper:  Dayhoff MO, Schwartz RM, and Orcutt BC, A Model of Evolutionary Change in Proteins. 1978, In Dayhoff, M. O. [ed] Atlas of protein sequece and structure, supplement 3. National Biomedical Research Foundation, Washington, DC, pp. 345-352. [Link]

• Example FASTA formated protein sequence [Download]
• Lecture slides (Lecture 5 -in greek) [Download]
• 2nd package of notes. Covers fundamentals of Sequence database search. Heuristics (FASTA, BLAST). Assessing statistical significance and some example applications. [Download]
• Paper: Lipman DJ and Pearson WR, Rapid and Sensitive Protein Similarity Searches. Science, 1985, Vol 227, Issue 4693, 1435-1441.
• Paper: Pearson WR and Lipman DJ, Improved Tools for Biological Sequence Comparison. PNAS, 1988, 85(8), 2444-2448. [Download]
• Paper: Altschul SF, Gish W, Miller W, Myers EW and Lipman DJ, Basic local alignment search tool. J. Mol. Biol., 1990, 215(3), 403-410. [Download]
• Paper: Altschul SF, Madden TL, Schäffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ, Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res.  1997, 25(17):3389-3402. [Download]
• Paper: McGinnis S and Madden TL, BLAST: at the core of a powerful and diverse set of sequence analysis tools. Nucleic Acids Res.  2004, 32(Web server issue):W20-W25. [Download]

• Lecture slides (Lecture 5 -in greek) [Download]
• 1st package of notes. Covers an introduction in biological macromolecular sequences and computational methods for sequence similarity analysis. (In greek) [Download]
• Paper: Needleman SB and Wunsch CD, A general method applicable to the search for similarities in the amino acid sequence of two proteins, J Mol Biol. 1970, 48(3):443-53. [link]
• Paper: Smith TF and Waterman M, Identification of common molecular subsequences, J Mol Biol. 1981, 147(1):195-197. [link]
• Paper: Gotoh O, An improved algorithm for matching biological sequences, J Mol Biol. 1982, 163(3): 705-708. [link]