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It og Sundhed
Thomas Nordahl Petersen, Associate Professor
Center for Biological Sequence Analysis, DTU
Mail: [email protected]
Lectures and exercises
Lectures: 915 - 12 room 062
Exercises: 13 - 16 room 062
Wireless network: https://auth.wireless.dtu.dk/index.cgi
Course days once a week (Break during christmas from Dec 15)
Written exam Jan 26 - 2012
Undervisning er på dansk, men undervisningsmateriale er fortrinsvis på engelsk.
Teachers
Thomas Nordahl Petersen
Henrik Nielsen
Anders Gorm Pedersen
Bent Petersen
Kasper Nielsen
Thomas Blicher
This is a hands-on course
• The major part of the course is computer exercises
• We get to use the actual methods• We get to use “live” online database
Everything is linked from the course programme
Readings, slides and hand-outs
Teaching material
Outline of the course
• Topics will cover a general introduction to bioinformatics– Evolution– DNA / Protein and amino acids– Alignment and scoring matrices
• How does it work & what are the numbers
– Visualization of multiple alignments• Phylogenetic trees and logo plots
– Commonly used databases• Uniprot/Genbank & Genome browsers• Genotype, phenotype & SNP’s
– Protein 3D-structure & homology modeling– Artificial neural networks & case stories– Practical use of bioinformatics tools– Sequence information and Logo plots
Outline of the course
The Amino Acids
Asn (N)
Asp (D)
Gln (Q)Glu (E)
His (H)
Lys (K)
Arg (R)
Tyr (Y)
Trp (W)
Phe (F)
Gly (G)Pro (P)
Ile (I)
Met (M)
Leu (L)
Ala (A)
Val (V)
Ser (S)
Cys (C)
Thr (T)
Automated sequencing
• The major break-through
of sequencing has
happended through
automation.
• Fluorescent dyes.
• Laser based scanning.
• Capillary electrophoresis
• Computer based base-
calling and assembly.
Images: http://www.idtdna.com/support/technical/TechnicalBulletinPDF/DNA_Sequencing.pdf
CE
NT
ER
FO
R B
IOLO
GIC
AL
SE
QU
EN
CE
AN
ALY
SIS
Theory of evolution
Charles DarwinCharles Darwin1809-18821809-1882
Phylogenetic tree
Sequence alignment - Blast
Sequence alignment - Blast
BLAST Exercise
Genome browsers - UCSC
Intron - Exon structure
Single Nucleotide polymorphism - SNP
Genome browsers - Ensembl
Protein 3D-structure
Protein 3D-structure
Neural NetworksFrom knowledge to information
Protein sequence Biological feature
Prediction of biological featuresSurface accessible
Predict surface accessible fromamino acid sequence only.
Logo plots
Logo plots
Logo plots
Information content, how is it calculated - what does it mean.
Written Exam
