Bioinformatics (and Constraints)

03/07/00


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Table of Contents

  1. Bioinformatics (and Constraints)

  2. Based on material jointly developed with

  3. Contents

  4. What is Bioinformatics

  5. Related but different...

  6. Human genome sequenced! 23 June 2000

  7. An advance or ???

  8. Issues

  9. What’s in the draft genome sequence?

  10. Bioinformatics is about:

  11. Aim of research in Bioinformatics

  12. Flood of data! (SWISSPROT)

  13. How can we analyse the flood of data ?

  14. Using the genome

  15. Molecular biology: flow of information DNA ? RNA ? Protein ? Function

  16. DNA double helix

  17. DNA base-pairs

  18. DNA

  19. Some facts...

  20. Gene structure

  21. DNA (gene) ? RNA ? Protein

  22. Numbers of genes

  23. Genetic code

  24. Translation

  25. Nucleotide sequence

  26. Protein (amino acid) sequence

  27. Protein structure

  28. Protein structure

  29. Proteins

  30. DNA-protein interaction

  31. Human genetic variations (Single Nucleotide Polymorphisms)

  32. Human individuality

  33. SNP implicated in coronary disease

  34. The Central Dogma of information flow in biology

  35. A Holy Grail

  36. 3 main classes of problem areas

  37. Current problem areas

  38. Protein folding problem (Structure prediction)

  39. Protein docking and ligand binding

  40. Binding sites

  41. Protein docking

  42. Protein docking approaches

  43. Next...

  44. Search and pattern discovery Sequences (DNA, RNA) Structure (RNA, protein)

  45. Sequence search & alignment

  46. Sequence alignment problem

  47. Alignment - Gaps

  48. Alignment via dynamic programming

  49. Human nucleotide sequence

  50. BLASTN results

  51. PSI-BLAST (position specific iterated)

  52. Pattern discovery in biosequences

  53. Protein families

  54. Protein family analysis

  55. Multiple vs. pairwise comparison

  56. Patterns and alternative representations

  57. PROSITE profiles

  58. Discrete patterns

  59. Biosequences - general

  60. PROSITE

  61. PROSITE patterns

  62. PROSITE examples

  63. Learning

  64. Example family (zinc finger c2h2)

  65. Example property

  66. Various ways of using pattern matching for family characterization

  67. Clean / Noisy Data

  68. True positives, true negatives, false positives, false negatives

  69. Approaches to pattern discovery

  70. Pattern driven algorithms

  71. Sequence driven approach

  72. Sequence driven algorithms

  73. RNA structural patterns

  74. Possible patterns

  75. Stem loops

  76. Pseudo-knot

  77. Protein patterns (motifs)

  78. Topological pattern discovery (Pattern-driven)

  79. Topological pattern discovery - maximal cliques

  80. CATH hierarchy

  81. CATH database hierarchy

  82. Structure comparison

  83. Structure comparison

  84. Dendrogram of comparisons

  85. Phylogenetic Trees

  86. Evolution

  87. Phylogenetic Trees

  88. Orthologue ?-haemoglobins

  89. Unrooted tree

  90. Biochemical Networks

  91. Chemical Reaction

  92. Enzymatic catalysis

  93. Inhibition/Activation

  94. Metabolic Step

  95. Methionine Biosynthesis in E.coli

  96. High-level Abstraction

  97. Networks - qualitative computation

  98. Computation over networks

  99. Array technology

  100. Yeast array

  101. PPT Slide

  102. Analysis of array data

  103. Detailed analysis...

  104. Discretizing the gene expression measurement space

  105. More data related issues...

  106. Skills and people

  107. Getting involved

  108. Resources www.soi.city.ac.uk/~drg/bioinformatics/resources.html

  109. Reading www.soi.city.ac.uk/~drg/bioinformatics/reading.html

  110. Reading

 Author: David Gilbert

Email: drg@soi.city.ac.uk

Home Page: http://www.cs.city.ac.uk/~drg

Resources

Reading

Postscript slides

PDF slides

Summary in English

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