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|
Computer exercises: general instructions
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| Tuesday 5/2 | S.
Brunak: Introduction.
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| L.J.
Jensen:Sequence Comparison
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| L.J.
Jensen: Pairwise
alignment and database searches I
(Durbin et al: Chapter 2)
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| Tuesday 12/2 |
A.G.Pedersen:
Multiple Alignment
(Durbin et al., chapter 6)
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|
A.G. Pedersen:
Phylogeny (Case Study: HIV)
Se lecture notes and paper on phylogeny
in binder.
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| Tuesday 19/2 | L.J.
Jensen: Pairwise
alignment and database searches II
(Durbin et al: Chapter 2)
|
| A.
Krogh: Weight matrices, regular expressions, and hidden Markov models.
See Introduction to Hidden Markov Models in binder
|
| Tuesday 26/2 | A.
Krogh: Hidden
Markov Models and Profile HMMs.
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| Tuesday 5/3 | A.
Krogh: Genome
Projects and Gene Finding.
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| Tuesday 12/3 | S.
Brunak:
Non-linear prediction by neural networks, sequence and category
representation, internal representation of sequence space,
signal peptide prediction, cross-validation and performance measures.
(Baldi and Brunak: Chapter 5 and 6.4, binder: Linjedeling med neuralt netvaerk)
|
| Tuesday 19/3 | S.
Brunak: Neural network model of the genetic code, intron splice site
prediction, neural network weight analysis,
training a neural network for protein secondary
structure prediction.
(Baldi and Brunak: Chapter 6)
|
| | Ramneek Gupta:
Predicting post-translational modifications using neural networks.
See slides on PTMs in binder
Performance evaluation
|
Passover
|
| Tuesday 2/4 | S.
Brunak: Prediction of protein secondary and tertiary structure,
protein function
(Baldi and Brunak: Chapter 6)
|
| Tuesday 9/4 | D.
Ussery:
DNA
symmetry elements and their meanings
See binder for papers on atlases.
|
| D.
Ussery:
A DNA Structural Atlas for Escherichia coli
|
| Tuesday 16/4 | S. Knudsen:
Analysis of
DNA Microarray Data
(Baldi and Brunak: pp 5-11; Binder: Analysis of DNA Array Data.
|
| N.
Tolstrup, Exiqon A/S: Guest Lecture -
Bioinformatics in an industrial setting
|
| Tuesday 23/4 | Start of individual projects. Show up for lecture
only if you have not yet signed up on web.
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| 23/4 - 14/5 |
Individual Projects
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| Tuesday 14/5 | Reports due
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|
Literature: |
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Go to:
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