Genomics and bioinformatics
Schedule for the course
Genomics and bioinformatics
IA = Room/Computer Lab Ivar Arosenius, Medicinareg. 5
KN = Room/Computer Lab Karl Nordström, Medicinareg. 5
A selection of links to other sources
- Home assignment : Describe your own research project in a few sentences and then go on to discuss how in that project you would be able to use one or more of the techniques described in this course. Do not write more than two pages!
9.00-12.00 Lecture and practical : Introduction to information resources UCSC lab(TS/MDL)
For reference a selection of databases and resources are shown here.
13.00-17.00 Lecture and practical : Introduction to information resources UCSC lab(TS/MDL)
9.00-12.00 Lecture, introduction to information resources, cont. and practicals NCBI lab (TS/MDL) and Galaxy lab(TS/MDL)
13.00-17.00 Lecture, introduction to information resources, cont. and practicals NCBI lab and Galaxy lab (TS/MDL)
9.00-12.00 Lecture and practical : Sequence alignment methods (TS/MDL).
Download njplot here if it is not already installed on your computer.
13.00-17.00 Lecture and practical : Sequence alignment methods (TS/MDL)
9.00-12.00 Lecture and practical : Applications of multiple alignments: Patterns/Profiles/Pfam and assigning functions to genes and proteins (TS/MDL).
13.00-17.00 Lecture and practical : Applications of multiple alignments: Patterns/Profiles/Pfam and assigning functions to genes and proteins (TS/MDL)
09.00-12.00 Demonstration and practical: Introduction to Unix enviroment used in bioinformatics and NGS.
Find answers to the exercises here.
Book chapter being a short introduction to Unix will be handed out (and is not available from this page).
Download the MobaXterm SSH client here (select portable edition) (TS).
13.00-17.00 Lecture and NGS practical: Exome sequencing
and short presentation of Genomics and Bioinformatics Core Facility resources (MDL).
At 14.00: Visit at Genomics Core Facility to see NGS equipment.
09.00-12.00 Lecture and practical: Genomes - assembly, gene finding, annotation and gene ontology. (TS)
13.00-17.00 Lecture and NGS practical ChIP-Seq (MDL/ZS)
09.00-12.00 Introduction and supervised practical: NGS - RNA-Seq (EL)
13.00-17.00 Practical NGS : Exome sequencing - variant visualization - IGV (MDL)
09.00-12.00 Non-supervised practicals: Gene prediction, continued from 18/3 and Gene Ontology practical.
If you cannot follow the links in the pdf document, here they are:
http://www.cbs.dtu.dk/chipcourse/Exercises/Ex_GO/GOexercise11.php (CBS exercises)
http://bio.biomedicine.gu.se/courses/vt13/ycc.c2.txt (the cluster 2 genes)
http://www.psb.ugent.be/cbd/papers/BiNGO/Home.html (BiNGO home page)
http://bio.biomedicine.gu.se/courses/vt13/batch.txt (list of genes for batch analysis)
http://www.psb.ugent.be/cbd/papers/BiNGO/Tutorial.html (Another BiNGO tutorial)
9.00-10.00 Lecture: The human microbiome (FB)
10.15-12.00 Lecture : Methods in phylogeny (TS).
13.00-17.00 Molecular phylogeny practical (TS)
09.00-12.00 Lectures : Molecular diagnostics, resistance (ML) Viral evolution and recombination (PN)
13.00-14.00 Lecture : Phylogeny, genotypes, hepatitis (HN)
- Students need to complete all practicals as well as the home assignment
Resources - software etc
- TS Tore Samuelsson
- MDL Marcela Davila Lopez
- ZS Zsolt Szilagyi
- EL Erik Larsson
- FB Fredrik Bäckhed
- ML Magnus Lindh
- PN Peter Norberg
- HN Helene Norder