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Department of
Computer Science and
Electronics
Gadjah Mada University
© Afiahayati
Courses
You do not need A-level biology for the course
An opportunity to:
– Use some of the most interesting computational
techniques to solve some of the most important and
rewarding questions
To give an introduction to
– Modern bioinformatics practices
– With an emphasis on computational aspects
To produce bioinformaticians
– Able to complement biologists
They use the algorithms, we design and tweak them
Two important areas
– Protein structure prediction
– Data mining bioarray informatics
Hirarki Informasi Kesehatan
What is…?
Bioinformatics
– Applying computational techniques to biology data
Medical informatics
– Applying computational techniques to medical data
Chemo-informatics
– Applying computational techniques to chemical data
Structural Genomics
Predictive toxicology
Drug trial Data
Medical diagnosis
Patient Record Data
Lecture 2
DNA sequence
codes for
(split into genes)
Amino Acid
Sequence
folds into has
Protein
3D
Structure
dictates Protein determines
Function
Cell
Activity
Good and Bad News
Without indels
Hamming distance
Scoring schemes
– Certain changes in sequence more likely
Due to chemical properties of the residues
BLAST algorithm
– Idea: match local regions and expand
– Seven part process
Lecture 4
B F
Lecture 5
Searching Databases
Multiple sequence
alignment algorithms
– Profiles
– PSI-BLAST
Lectures 7 & 8
Machine Learning
Machine learning (inductive reasoning)
– Automatic proposing of hypotheses based on data
– Has many applications in bioinformatics
Including protein structure prediction
Example: predictive toxicology
– Given: set of toxic drugs and a set of non-toxic drugs
– Given: background information (chemistry, etc.)
– Produces: hypothesis why drugs are toxic
Overview of machine learning
– Aims, techniques, methodologies, representations
Artificial neural networks
Evaluating Learned Hypothesis
How do we know that a rule/hypothesis
– Reflects something interesting, not a coincidence?
Define errors
Use statistics to define confidence intervals
Show that one learning algorithm
– Outperforms another algorithm
Lecture 10
Protein function
– From the protein’s fold
Look at:
– Folds, functions, evolution of
structure and function
Protein Structure Prediction