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Schedule for distance course in bioinformatics

Section Text To Read Assignments
Introduction
  1. The Genomes
    none
Databases
  1. Intro to databases
  1. Entrez
  2. NCSA biology workbench
Sequence alignments
  1. Biological motivation
  2. Introduction
  3. Dynamic programming
  4. Pairwise alignments
  5. Substitution matrixes
  1. How do I align two proteins ?
Database searches
  1. Using alignments to search databases.
  2. Statistics of sequence alignments.
  3. Heuristic search methods
  4. Implementations
  1. Detection of related proteins.
Multiple sequence alignments
  1. Introduction
  2. Profiles.
  3. psiblast
  4. clustalW
  5. Hidden Markov Models
  6. Pfam
  1. Does my protein belong to a known protein family?
  2. PSIBLAST
  3. PSIBLAST
Sequence analysis
  1. Neural Networks.
  2. LOGOs.
  1. How do I detect a pattern in a protein
  2. Logo creations.
Secondary structure predictions
  1. Secondary structure predictions
  2. Membrane protein structures
  1. Can I predict the secondary structure of a protein?
  2. Can I predict what part of a protein is in a membrane?
Protein structure prediction
  1. Protein fold recognition
  2. Homology modelling
  1. Is my protein related to a protein of known structure?
  2. Structural databases.
Molecular evolution
  1. Dinosaur
Microarrays
Metabolic modelling
Arne Elofsson
Last modified: Tue Oct 15 09:00:02 CEST 2002
Arne Elofsson
Stockholm Bioinformatics Center,
Department of Biochemistry,
Arrheniuslaboratoriet
Stockholms Universitet
10691 Stockholm, Sweden
Tel: +46-(0)8/5537 8568
Fax: +46-(0)8/5537 8214
Hem: +46-(0)8/6413158
Email: arne@sbc.su.se
WWW: /~arne/