3-16 March 2020

SB II, Colonel-Kleinmann-Weg 2,

3. Stock, Raum-Nr. 03-544

Please, note that eating in the room where we will teach is strictly forbidden. In the SB II building there is a room across the main entrance that you can use for eating.

 

Day 1 / 3 March Tuesday / 9:00 - 17:00

Biostatistics / Statistical genetics

Presentation: biostatistics course_2020

R-script: Introduction-R-Task-1.R (download and rename to remove the .txt extension)

Solutions: Introduction-R-Task-1-Solutions.R (download and rename to remove the .txt extension)

Day 2 / 4 March Wednesday / 9:00 - 17:00 

Protein coding genes in genomic sequences, Homology I

Homology II, Multiple sequence alignment I

 

Day 3 / 5 March Thursday / 9:00 - 17:00

Multiple sequence alignment II

Phylogenetic analysis

• Seaview --> Steps:
  1. Download from --> seaview
  2. Decompress the folder
  3. Click on file "seaview_WINDOWS.exe"
  4. Extract
  5. Go in folder "seaview"
  6. Click on "seaview.exe"
• Exercise 12 -> snakes.fasta
• Exercise 13 -> file1.fasta
• Exercise 14 -> file2.fasta
• Exercise 15 -> file3.fasta
• Exercise 16 -> file4.fasta

*Solutions for exercises from Day 2 and Day 3 --> Exercises-Master2020_SHORT

 

Day 4 / 6 March Friday / 9:00 - 17:00

Programming I

• R-Course-2020-Intro.pdf
• Link to online R tutorial
• datasets.zip

Programming II

 

Day 5 / 9 March Monday / 9:00 - 17:00

Programming III

• Link to solutions (1-4)
• Link to solutions (5)

Programming IV

• Link to online additional exercises
• Link to solutions (6)
• Additional files (do not download manually):
  • records.csv.gz
  • users.csv.gz
  • users2018.tsv.gz
  • AVGduration.tsv.gz
• Link to online 2nd additional exercises (Genes and Proteins)

Day 6 / 11 March Wednesday / 9:00 - 17:00

Protein structure, homology modelling

Lecture notes (Enrique Muro): MuroMB2020_2

Low complexity regions / repeats

Presentations: lesson1_chimera_5 | lesson2_domains_5 | lesson3_model3D_6_st | lesson4_repeats_2_st | lesson5_repeatsdbs_3_st

Day 7 /  12 March Thursday / 9:00 - 17:00

Kinetic modeling of protein dynamics

Proteomics

 

Day 8 / 13 March Friday / 9:00 - 13:00

RNA-seq

 

Day 9 / 16 March Monday / 10:00 - 17:00

Seminars day

 

Files:

tutorial_scientific_article_presentation

Main points of days 2 and 3 (Enrique M. Muro)

Links:

Get a random reviewed Homo sapiens sequence from UniProt

Protein Data Bank (PDB): http://www.rcsb.org/

PFAM: https://pfam.xfam.org/

UniProt: https://www.uniprot.org/

ClustalOmega: https://www.ebi.ac.uk/Tools/msa/clustalo/

T-Coffee: http://tcoffee.crg.cat/

T-REX: http://www.trex.uqam.ca/

Repeats db: http://repeatsdb.bio.unipd.it/

dAPE: http://cbdm-01.zdv.uni-mainz.de/~munoz/polyx/

Dotlet: http://dotlet.vital-it.ch

Aquaria: http://aquaria.ws/