Bioinformatics in practice, Faroe Islands 2024

This is the home page for week 45+46 of the "Bioinformatics in practice" course, Faroe Islands 2024. These five days are taught by Henrik Nielsen and Bent Petersen.

Monday November 4

Morning: Introduction, plain text files and taxonomy databases

Lectures:

• Introduction to bioinformatics and computers - Henrik
• Evolution & taxonomy - Bent

Exercises:

• Plain text files and Geany
• Taxonomy databases

Afternoon: GenBank

Lecture: Biological information, DNA, sequencing, and GenBank - Henrik

Handout exercise: "Base-calling" (PDF) / On-screen version (PDF)

Materials:

• GenBank + FASTA format (PDF)
• Eukaryotic gene structure overview (PDF)

Exercise: Using the GenBank database

Wednesday November 6

Morning: Translation and UniProt

Lecture: Proteins: data and databases - Henrik

Materials:

• Virtual Ribosome — software article (PDF)
• Proteins, levels of structure (PDF)
• Eukaryotic gene structure overview (PDF)

Exercises:

• Exercise: Translation - Virtual Ribosome
• Exercise: The protein database UniProt

Afternoon: Protein structure, PDB & PyMOL

Lecture: Protein 3D structure - Bent

Software for installation: PyMOL

Note: you will need a license file which we will provide via Zoom.

Exercises:

• PyMol tutorial (PDF)
• Protein Structure and Visualization

Thursday November 7

Morning: Pairwise alignment

Lecture: Pairwise alignment - Henrik

Handout exercise: Alignment scores

Exercise: Pairwise alignment — Answers

Wrap-up: Pairwise alignment revisited

Afternoon: Sequence database searching with BLAST

Lecture: Introduction to BLAST - Bent

Exercise: Exercise: BLAST — Answers

Wrap-up: BLASTN vs BLASTP

Wednesday November 9

Morning: Sequence information and logo plots

Lecture: Sequence information and logo plots - Henrik

Materials: "Information theory primer" (PDF)

Handout exercise: How to construct sequence logos — Answer

Exercise: DNA and Peptide LOGOs — Answers

Afternoon: Profile searching with PSI-BLAST

Lecture: PSI-BLAST - Bent

Exercise: PSI-BLAST — Answers

Friday November 11

Morning: Multiple alignments

Lecture: Multiple Alignments - Henrik

Materials: RevTrans (article, PDF)

Exercise: Multiple Alignments — Answers

Afternoon: Phylogenetic trees

Lecture: Phylogenetic trees - Bent

Handout exercise: Reconstruction of distance tree

Software for installation: FigTree tree-viewer

IMPORTANT NOTE for Windows users: Download the .zip file (FigTree.v1.4.4.zip) and unpack it. Then, go to the "lib" subfolder and double-click the .jar file. The .exe file may not work.

Exercise: Exercise: Phylogeny — Answers