Advanced Bioinformatics

Course description

An introduction to the fundamental theory and practice of bioinformatics.

Goals for the course: The course will familiarize students with the fundamental principles of bioinformatics. By the end of the course, students will
have a working knowledge of a variety of topics important in bioinformatics, and a grasp of the underlying principles that is adequate for them to
evaluate and use new bioinformatics methods as they arise in the future.

Course Requirements:

• Prerequisites: A familiarity with the concepts of bioinformatics.
  Although there are no formal course prerequisites, you should have at least one prior upper division undergraduate course (or better) in
  bioinformatics skills.

• For this course, students will be required to read in advance a (or several) particular articles. Additional reading material may also be
  assigned by each instructor.

• Reference books:
  (1) “Algorithms on Strings, Trees, and Sequences: Computer Science and Computational Biology”. Dan Gusfield, Cambridge University Press.
  (2) “Introduction to Computational Molecular Biology”. Setubal, Meidanis, PWS Publishing.
  (3) “Biological Sequence Analysis: Probabilistic models of proteins and nucleic acids”. Durbin, Eddy, Krogh, Mitchison. Cambridge University
         Press.

Syllabus

The assigned reading materials will be available in Acrobat (pdf) format.

1. 授課對象：生物資訊研究所博士班　　　　　　　 時　　間：每週二上午10:10-12:00 地　　點：傳醫大樓乙棟五樓516室		負責教師姓名：楊永正、張傳雄                                    聯 絡 電 話 ：(02) 28267128                                   張傳雄教師: (02) 28267316
   週次	日期		討論主題	時數	教師姓名	Reading Assignments
   1 2   3 4 5 6 7 8 9 10   11 12 13 14 15 16 17 18	9/15 9/16   9/23 9/30 10/07 10/14 10/21 10/28 11/04 11/11   11/18 11/25 12/02 12/09 12/16 12/23 12/30 01/06		Systems Biology - Symposium Systems Biology - Workshop First Section Topic: * Sequence Comparison *       Dot Plot Dynamic Programming (Global & Local) Scoring Matrices FASTA BLAST Multiple Sequence Alignment Suffix Tree & MUMmer Midterm Report Second Section Topic: * Pathway Analysis * TBA TBA TBA TBA TBA TBA TBA Final Report	2 2   2 2 2 2 2 2 2 2   2 2 2 2 2 2 2 2	楊永正 張傳雄   張傳雄 張傳雄 張傳雄 張傳雄 張傳雄 張傳雄 張傳雄 張傳雄   楊永正 楊永正 楊永正 楊永正 楊永正 楊永正 楊永正 楊永正	Article # 01 Article # 02, 03 Article # 08, 09 Article # 10, 11 Article # 12, 13 Article # 18, 19 Article # 20, 21     Article # 22, 23 Article # 24, 25 Article # 26, 27 Article # 28, 29 Article # 30, 31 Article # 32, 33 Article # 34, 35

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   Grading

   Midterm

   Midterm:  There will be an in-class Presentation Report on November 11, and it will be worth fifty points.

   Final

   Final:  There will be an in-class Presentation Report on January 6, 2004, and it will be worth fifty points.

   ---

   Reading assignments
   
   * SEQUENCE COMPARISON*

   Dot Plot
       1. Gibbs, A. J. & McIntyre, G. A. (1970).
           The diagram method for comparing sequences. its use with amino acid and nucleotide sequences.
           Eur. J. Biochem. 16, 1-11.
           [pdf]
   
   Dynamic Programming
       Global Alignment:
       2. Needleman, S. B. & Wunsch, C. D. (1970).
           A general method applicable to the search for similarities in the amino acid sequence of two proteins.
           J. Mol. Biol. 48, 443-453.
           [pdf]

       Local Alignment:
       3. Smith, T. F. & Waterman, M. S. (1981).
           Identification of common molecular subsequences.
           J. Mol. Biol. 147, 195-197.
           [pdf]
   
   Statistical Significance of Sequence Alignments & others
       4. Gotoh, O. (1982).
           An improved algorithm for matching biological sequences.
           J. Mol. Biol. 162, 705-708.
           [pdf]
   
       5. Waterman, M. (1994).
           Estimating statistical of sequence alignments.
           Phil.Trans.R.Soc.Lond B 344, 383-390.
           [pdf]
   
       6. Altschul, S.F. & Gish, W. (1996).
           Local alignment statistics.
           Meth. Enzymol. 266, 460-480.
           [pdf]
   
   Substitution Matrices
       7. Henikoff, S. & Henikoff, J. G. (1993).
           Performance evaluation of amino acid substitution matrices.
           Proteins: Struct., Funct., Genet. 17, 49-61.
           [pdf]
   
       PAM:
       8. Dayhoff, M. O., Schwartz, R. M. & Orcutt, B. C. (1978).
           A model of evolutionary change in proteins. matrices for detecting distant relationships.
           In Atlas of protein sequence and structure, (Dayhoff, M. O., ed.), vol. 5, pp. 345-358.
           National biomedical research foundation Washington DC.
           [pdf-1] & [pdf-2]

       BLOSUM:
       9. Henikoff, S. & Henikoff, J. G. (1992).
           Amino acid substitution matrices from protein blocks.
           Proc. Natl. Acad. Sci. USA, 89, 10915-10919.
           [pdf]
   
   FASTA
       10. Lipman DJ, Pearson WR. (1985).
             Rapid and sensitive protein similarity searches.
             Science 227(4693), 1435-1441.
             [pdf]
   
       11. Pearson WR, Lipman DJ. (1988).
             Improved tools for biological sequence comparison.
             Proc Natl Acad Sci U S A. 85(8), 2444-2448.
             [pdf]
   
   BLAST
       12. Altschul, S. F., Gish, W., Miller, W., Myers, E. W. & Lipman, D. J. (1990).
             Basic local alignment search tool.
             J. Mol. Biol. 215, 403-410.
             [pdf]
   
       13. Altschul, S.; Madden, T.; Schaffer, A.; Zhang, J.; Zhang, Z.; Miller, W.; and Lipman, D. (1997).
             Gapped BLAST and PSI-BLAST: a new generation of protein database search programs.
             Nucleic Acids Res. 25, 3389-3402.
             [pdf]
   
       14. Altschul, S.F. & Koonin, E.V. (1998).
             Iterated profile searches with PSI-BLAST - a tool for discovery in protein databases.
             Trends Biochem. Sci. 23, 444-447.
             [pdf]
   
       15. Zhang Z, Schaffer AA, Miller W, Madden TL, Lipman DJ, Koonin EV, Altschul SF. (1998).
             Protein sequence similarity searches using patterns as seeds. (PHI-BLAST)
             Nucleic Acids Res. 26, 3986-90.
             [pdf]
   
   Profile Analysis
       16. Gribskov, M., McLachlan, A. D. & Eisenberg, D. (1987).
              Profile analysis: Detection of distantly related proteins.
              Proc. Natl. Acad. Sci. USA, 84, 4355-4358.
             [pdf]

   Multiple Alignment
       17. Lipman, D. J., Altschul, S. F. & Kececioglu, J. (1989).
            A tool for multiple sequence alignment.
            Proc. Natl. Acad. Sci. USA, 86, 4412-4415.
             [pdf]
   
       18. Thompson JD, Higgins DG, Gibson TJ. (1994).
            CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific
            gap penalties and weight matrix choice.
            Nucleic Acids Res.  22, 4673-80.
             [pdf]
   
       19. Chenna R, Sugawara H, Koike T, Lopez R, Gibson TJ, Higgins DG, Thompson JD. (2003).
             Multiple sequence alignment with the Clustal series of programs.
             Nucleic Acids Res.  31, 3497-3500.
             [pdf]
   
   Suffix Tree & MUMmer
       20. Delcher AL, Kasif S, Fleischmann RD, Peterson J, White O, Salzberg SL. (1999).
             Alignment of whole genomes.
             Nucleic Acids Res. 27, 2369-2376.  
             [pdf]
   
       21. Delcher AL, Phillippy A, Carlton J, Salzberg SL. (2002).
             Fast algorithms for large-scale genome alignment and comparison.
             Nucleic Acids Res. 30, 2478-83.
             [pdf]
   
   
   * PATHWAY ANALYSIS*

Web sites

Sites mentioned in class

• Local Resources

• Key Bioinfo tools and sites