BIOINFORMATICS ​

METADATA ​

The teacher is not a biologist, but a computer scientist.

EXAM ​

Written and oral (if you pass the written part) or 2 partials.

• Written part (core of the exam): Open questions and exercises.
• (15 minutes, 3 points, i.e. 1 week of work) oral part or assignment to present in class (group in 2/3 people)
  • depends on the teacher (probably it will be an assingment), we will know this a mid course (november)

In short: Or:

• Written part -> oral
• Presentation + Written part
• written part + presentation

Materials ​

There is no a textbook to buy.

• Introduction to algorithms (Cormen)
• Algorithms on strings (Gusfield)
• Biologicalsequence analysis, probabilistic models and nucleic acids (Durbin)
• Bioinformatics-sequence and genome analysis (Mount)

Intro ​

Important to remember ​

• Bioinformatics applications generally have to deal with:
  • enormous amount of data
  • data which contains redunadncy and errors
  • imcomplete information
  • rules with many exceptions
  • heuristic solutions
• It is nevessary to have a deep knowledge of the biological problem to be solved.
• It is necessary to work together with biologists, statisticians, ...
• It is a difficult process beacause we don't speak the same language.

Bioinformatics syllabus ​

• Introduction to molecualr biolagy
  • DNA, RNA, Proteins
• Exact sequence search
  • pattern preprocessing (FA algorithm, KMP algorithm)
  • text preprocessing (suffix trees, suffix array)
• Approximate sequence search
  • Pair alignment (heuristics, scores, exact methods for global and local alignment)
  • Multiple alignment
• Genome sequencing
  • Techlogies and techniques (encode some partes of molecules in strings)
• Protein structure determination
  • introduction
• Phylogenetic trees
  • characteristics and inference methods (compare genes of different species)
• Sequence modelling
  • HMM for modelling biological data
• Systems biology
  • general introduction and examples

Biological background ​

Outline ​

• DNA and genome
• Proteins

Metaphor: DNA as software ​

• Software -> a component specialized to contain data and commands to interpret then (DNA)
• Hardware -> a component able to interpret it and to traslate it iinto actions (cell).

DNA ​

DNA (Deoxyribose Nucleic Acid) is the nucleic acid which encodes the genetic program of both prokaryotes (bacteria and archea) and eukaryotes (animales and plant)

Trasforming principle ​

Experiment:

• non patogenous bacteria -> mouse -> alive
• patogenous bacteria -> mouse -> dead
• killed patogenous bacteria with heat -> mouse -> alive
• killed patogenous bacteria with heat + non patogenous bacteria -> mouse -> dead

This experiment showed that the transforming principle is the DNA. Previuosly they believed that proteins were responsible for carrying the genetic information.

Dna is a long polymer made from repeating units called nucleotides or bases 4 (loong chain of billion bases):

DNA/RNA bases:

• A: Adenine
• C: Cytosine
• G: Guanine
• T: Thymine (only in DNA)
• U: Uracil (only in RNA)

The DNA is a bounded by two strands of nucleotides which form a double helix. The bases are in the middle of the helix and they are bounded by hydrogen bonds. The hydrogen can be broken easily. Strands: are antiparallel. They are made by a sugar-phosphate backbone.

Pairs: A-T C-G

This means if we know one helix we can know the other one.

DNA replication ​

DNA polymerase is the enzyme which is responsible for the replication of DNA. It is able to read a DNA strand and to create a new one which is complementary to the original one.