Support materials biomedicine master March 2021

8-19 March 2021

By videoconference on

https://bbb.rlp.net/b/and-1hz-kz4-5fq

Day 1 / 8 March Monday / 9:00 - 17:00

Biostatistics / Statistical genetics

R-script: Basics_in_R_1.R (download and rename to remove the .txt extension)

Presentation: biostatistics course_2021

Exercises: excercises biostatistics

Day 2 / 9 March Tuesday / 9:00 - 17:00

Protein coding genes in genomic sequences, Homology I

Homology II, Multiple sequence alignment I

https://www.uniprot.org/uniprot/

https://genome.ucsc.edu/cgi-bin/hgBlat

https://genome-euro.ucsc.edu/cgi-bin/hgBlatcommand=start

Day 3 / 10 March Wednesday / 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"

 

Day 4 / 11 March Thursday / 9:00 - 17:00

Protein structure, homology modelling

Low complexity regions / repeats

Presentations: lesson1_chimera_6 | lesson2_domains_6 | lesson3_model3D_7 | lesson4_repeats_3

Data files: MR1_fasta

 

Day 5 /  12 March Friday / 9:00 - 16:30

Repeat databases / Disorder in proteins

Presentations: lesson5_repeatsdbs_4 | idp_course_with_answers

Seminars

 

Day 6 /  15 March Monday / 9:00 - 17:00

Programming I

Introduction slides: R-Course-2021-Intro

Tutorial: click here (includes all material)

If the link to the tutorial is broken, you can use the following link to download a ZIP archive containing the tutorial and required data files: 20210310_R_tuto_ggplot

Programming II

Extra exercises: click here

Day 7 / 16 March Tuesday / 14:00 - 17:00

(morning free)

Programming III

Day 8 / 17 March Wednesday / 9:00 - 17:00

Protein interaction networks

Presentations: Master_ProteinBiochemBioinfo_2021_PPIs_1_2_KL | Master_ProteinBiochemBioinfo_2021_PPIs_3_KL | Master_ProteinBiochemBioinfo_2021_PPIs_4_KL | Master_ProteinBiochemBioinfo_2021_PPIs_5_KL

Files: Kaplanis_28_genes | Kaplanis_28_genes_annotated | Kaplanis_285_genes | Kaplanis_285_genes_annotated

Related publications: Kaplanis_DDD_analysis_Nature2020 | Wang_RSU1_PHB2_PPI_curation_example_JBC2020

Proteomics

Presentation: Bioinformatics_VL_20210317_UD

Day 9 / 18 March Thursday / 9:00 - 17:00

RNA-seq

Seminars

 

Day 10 / 19 March Friday / 9:30 - 17:30

Seminars

 

Software required:

Please, install in your computer and test prior to the corresponding lesson. If you have problems installing any of the indicated software then email the corresponding contact person (in brackets).

Chimera: install current prodution release from https://www.cgl.ucsf.edu/chimera/download.html (protein 3D representation; Miguel Andrade)

JalView: install from http://www.jalview.org/getdown/release/ (alignment and structure representation; Miguel Andrade)

SeaView: (alignments and phylogenetic trees; Pablo Mier)

1. Download from: http://doua.prabi.fr/software/seaview
2. Decompress the folder
3. Click on file "seaview_WINDOWS.exe"
4. Extract
5. Go in folder "seaview"
6. Click on "seaview.exe"

R: (RNAseq analysis, Federico Marini) (ideally R >= 4.0.0, https://cran.r-project.org/) - latest version recommended (4.0.4 at the moment of writing)

RStudio: (RNAseq analysis, Federico Marini) (recommended)
https://rstudio.com/products/rstudio/download/, the free version is more than enough!

CRAN and Bioconductor (https://bioconductor.org/) packages: (RNAseq analysis, Federico Marini)

For the bulk transcriptome analysis:
# install the Bioc installer
install.packages("BiocManager")
# install Bioc version 3.12
BiocManager::install(version = "3.12")
# install specific Bioconductor packages BiocManager::install(c("pcaExplorer", "ideal", "GeneTonic", "macrophage", "org.Hs.eg.db", "clusterProfiler"), dependencies = TRUE)

Check all packages are installed by calling library("package_name") e.g.
library("DESeq2")
library("pcaExplorer")
library("ideal")
... should return no error

Cytoscape: (Protein networks; Katja Luck)

 

Files:

tutorial_scientific_article_presentation

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/

BLAT (UCSC): https://genome.ucsc.edu/cgi-bin/hgBlat

BLAT (UCSC european mirror): https://genome-euro.ucsc.edu/cgi-bin/hgBlatcommand=start

Blastp (NCBI): https://blast.ncbi.nlm.nih.gov/Blast.cgi?PROGRAM=blastp&PAGE_TYPE=BlastSearch&BLAST_SPEC=&LINK_LOC=blasttab&LAST_PAGE=blastp

Timetree: http://www.timetree.org/