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Computer exercises: general instructions
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| Tuesday 3/9 | S.
Brunak and S. Knudsen: Introduction.
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| A.G. Pedersen:
Pairwise
alignment
(W.R. Pearson, "Protein Sequence Comparison and Protein Evolution", binder,
p. 1-27)
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| Tuesday 10/9 |
A.G.Pedersen:
Database searching
(W.R. Pearson, "Protein Sequence Comparison and Protein Evolution", binder, p. 27-53)
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A.G. Pedersen:
Multiple alignment
(No reading required)
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| Tuesday 17/9 |
A.G. Pedersen:
Molecular Phylogeny
("Molecular Phylogenetics: Methods": chapter 5 from W.H.Li,
"Molecular Evolution". Xerox of this chapter is included in the binder)
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| Tuesday 24/9 |
N. Blom:
Gene Finding Exercises
Gene finding
("Finding the genes in genomic DNA",
C.B.Burge & S.Karlin (1998), Curr.Op.Struc.Biol. 8:346-354; in binder
; Optional background reading on Hidden Markov Models:
"An introduction to Hidden Markov Models for Biological Sequences"
A.Krogh (2002); in binder)
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| Tuesday 1/10 |
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)
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| Tuesday 8/10 |
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)
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| |
S. Brunak:
Predicting post-translational modifications using neural networks.
See slides on PTMs in binder
Performance evaluation
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Autumn holiday
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| Tuesday 22/10 |
S.
Brunak: Prediction of protein secondary and tertiary structure,
protein function
(Baldi and Brunak: Chapter 6)
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| Tuesday 29/10 |
D.
Ussery:
DNA
symmetry elements and their meanings
See binder for papers on atlases.
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| D.
Ussery:
A DNA Structural Atlas for Escherichia coli
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| Tuesday 5/11 |
S. Knudsen:
Analysis of
DNA Microarray Data
(Baldi and Brunak: pp 5-11; Binder: Analysis of DNA Array Data.
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N.
Tolstrup, Exiqon A/S: Guest Lecture -
Bioinformatics in an industrial setting
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| Tuesday 12/11 | Start of individual projects. Show up for lecture
only if you have not yet signed up on web.
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| 12/11-3/12 |
Individual Projects
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| Tuesday 3/12 |
Reports due
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Literature: |
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Go to:
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