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Bioinformatics 2

Notes

Where possible I shall post lecture notes the evening before the lecture. However, these may be revised prior to the lecture. Additional reading will be posted before or after the lecture as appropriate.

2005 notes are available for reference

Lecture Notes

Lecture 1 (Jan 11 2006) Introduction (pdf)
Introduction to Bioinformatics; Introduction to Sequence Alignment; Substitution Matrices; Gap Penalties.

Lecture 2 (Jan 18 2006) Pairwise Sequence Alignment; (pdf)
Dynamic Programming implementations for pairwise sequence alignment.
Manual Alignment Exercise
EBI BLAST and FASTA
NCBI BLAST
Example genes to play with: ADH & yuri

Lecture 3 (Jan 25 2006) Heuristic methods for alignment, sequence databases and multiple alignment. (pdf)
PDE4B sequences from public databases
DLG and human orthologues from public databases
ClustalW alignment of DLG and human orthologues
dbSNP
Millar et al 2005 paper on PDE and Schizophrenia, enter the PMID (number) into the link to connect: 16293762
Tarpey et al 2004 paper on Sap103/DLG3 and mental retardation again, use PMID 15185169 in the search box.

Lecture 4 (Feb 1 2006) Gene and Protein Prediction. (pdf)
InterPro
PredictProtein
Taverna
Primer on Protein Structure
Pictures, Movies and Tools for 3D Protein Models
Bioinformatics Current Table of Contents

Lecture 5 (Feb 8 2006) Malcolm Walkinshaw, Structure Based Drug Design.
Ribosome movie. Further reading material 1, 2, 3.

Lecture 6 (Feb 15 2006) Functional Genomics (pdf)

Lecture 7 (Feb 22 2006) Proteomics (pdf)
Further reading:
Rual et al 2005, Towards a proteome scale map of the human protein-protein interaction network
Milo et al 2002 paper on Network Motifs, enter the PMID into the link: 12399590
Pocklington et al (2006) paper on G2C project.

Lecture 8 (Mar 8 2006) Dirk Husmeier
Background reading:
Husmeier D., Dybowski R., and Roberts S. (2005) Probabilistic Modeling in Bioinformatics and Medical Informatics. (link) Springer Verlag Chapters 1,2 and 4.
Durbin, R. and Eddy, S. R. and Krogh, A. and Mitchison, G. (1998) Biological sequence analysis. Probabilistic models of proteins and nucleic acids. Chapter 3,7, 8.
Primer from 2005

Lecture 9 (Mar 15 2006) Chris Larminie, GSK

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