24 Nov. - 5 Dec. 2024

00-445 (N33) NatFak Hauptgebäude

 

Day 1 / 24 November Monday / 9:00 - 17:00

Proteins coded in genomes and protein annotations. Homology.

You are expected to take notes during the class. Also, we will write down (paper and a pen) some exercises during the class.

Before the course starts:

Be sure that you are ready to run Python and you are familiar with the JGU Jupyter server: https://cbdm-01.zdv.uni-mainz.de/~muro/teaching/p4b/em-book/c0_set_up/c0_jgu_jupyter_notebook_server.html We will use the "Biology environment" that has been set up for this class.

We will run some Python programs, review in advance the material we learned in the bachelor studies (only chapter 2): https://cbdm-01.zdv.uni-mainz.de/~muro/teaching/p4b/em-book/c2_printing_and_manipulating_text/c2_printing_and_manipulating_text.html

See this example where the whole proteome of SAR2 can be analyzed:

EM_gzip_fasta_averageProtein_sars2.txt (download and rename to change the .txt extension by .ipynb)

See this example where the average aa mass can be calculated:

EM_average_aa_mass.txt (download and rename to change the .txt extension by .ipynb)

See this example where the real average aa mass in a whole can be calculated:

EM_average_aa_mass_proteome_students.txt  (download and rename to change the .txt extension by .ipynb)

Or this other example where you can create a simple phylogenetic tree:

EM_simple_phylogenetic_tree.txt (download and rename to change the .txt extension by .ipynb)

For more functionality or in the case the JGU Jupyter server fails we will be ready to use colab. Then, open an account in colab from Google in advance: https://colab.research.google.com/

Some useful links we will use during the class:

• • UniProt -> https://www.uniprot.org/
  • UCSC: https://genome.ucsc.edu/
  • BLAT (UCSC): https://genome.ucsc.edu/cgi-bin/hgBlat
  • BLAT (UCSC European mirror): https://genome-euro.ucsc.edu/cgi-bin/hgBlat
  • NCBI -> https://www.ncbi.nlm.nih.gov/
  • NCBI BLAST -> https://blast.ncbi.nlm.nih.gov/Blast.cgi?PAGE=Proteins
  • Blastp (NCBI): https://blast.ncbi.nlm.nih.gov/Blast.cgi?PROGRAM=blastp&PAGE_TYPE=BlastSearch&BLAST_SPEC=&LINK_LOC=blasttab&LAST_PAGE=blastp
  • T-Coffee (MSA) -> https://tcoffee.crg.eu/
  • Clustal Omega -> https://www.ebi.ac.uk/jdispatcher/msa/clustalo
  • Seaview -> https://doua.prabi.fr/software/seaview
  • Dotlet: http://dotlet.vital-it.ch
  • NCBI taxonomy -> https://www.ncbi.nlm.nih.gov/taxonomy
  • Gene Ontology -> https://geneontology.org/
  • Quick Go -> https://www.ebi.ac.uk/QuickGO/help
  • AmiGO 2 -> https://amigo.geneontology.org/amigo
  • Timetree: http://www.timetree.org/

 

For the Seminars, I recommend reading: Ten Simple Rules for Making Good Oral Presentations.

Day 2 / 25 November Tuesday / 9:00 - 17:00

Protein interaction networks

Software required: Cytoscape

• Slides (Katja Luck): Master_ProteinBiochemBioinfo_2025_PPIs_1_2_KL_students | Master_ProteinBiochemBioinfo_2025_PPIs_3_KL_students | Master_ProteinBiochemBioinfo_2025_PPIs_4_KL | Master_ProteinBiochemBioinfo_2025_PPIs_5_KL
• Files (Katja Luck):
  • Cytoscape_tasks
  • GTEx_tissue_expression_Kaplanis_genes_285
  • Kaplanis_28_genes_annotated
  • STRING_input_28_genes
  • STRING_interactions_Kaplanis_285
  • STRING_questions

 

Slides (Emily Vagiona): MSc_module_Proteinbiochemie_und Bioinformatik_2025_Vagiona

 

Day 3 / 26 November Wednesday / 9:00 - 17:00

Pairwise alignment. Multiple sequence alignment. Phylogeny.

The very same requirements as "day 1 (25 Nov)".

 

Day 4 / 27 November Thursday / 9:00 - 13:00

Protein structure, representation.

Software required: Chimera

Slides (Andrade): 

 

Day 5 / 28 November Friday / 9:00 - 17:00

Programming with R (I).

Software required: R / RStudio Desktop

Tutorial (Johannes Wolter):

Dynamic modelling.

Slides (Alex Anyaegbunam):

 

Day 6 / 1 December Monday / 9:00 - 17:00

Protein domains, disorder.

Software required: Chimera / JalView

Data files (Andrade; repeats): MR1_fasta

Slides (Andrade): 

Slides (Eric Schumbera):

 

Day 7 / 2 December Tuesday / 9:00 - 17:00

Programming with R (II).

Link to download files (Mert Cihan): https://seafile.rlp.net/d/7e4e8082f1ce487d9d97/

Data Mining

Exercise material (Piyush More):

Slides (Piyush More):

 

Day 8 / 3 December Wednesday / 9:00 - 17:00

Proteomics.

Slides (Ute Distler):

Slides (Stefan Tenzer):

Tissue 3D printing (MPI-P).

Maria Villiou - bring laptop or tablet

 

Day 9 / 4 December Thursday / 9:00 - 13:00

RNAseq.

Slides (Federico Marini):

 

 

Day 10 / 5 December Friday / 9:00 - 17:00

Programming with R (III).

Data files (Mert Cihan):

Slides (Mert Cihan):

 

 

 

 

Software required:

Please, install in your remote desktop and test prior to the corresponding lesson using https://apps.zdv.uni-mainz.de/. If you have problems installing any of the indicated software then email the corresponding contact person (in brackets).

R: (Programming with R; Johannes Wolter)

RStudio Desktop: (Programming with R; Johannes Wolter)

Chimera: (protein 3D representation; Miguel Andrade)

JalView: (alignment and structure representation; Miguel Andrade)

Cytoscape: (Protein networks; Katja Luck)

 

Links:

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

UniProt: https://www.uniprot.org/