Bioinformatics in practice, Faroe Islands 2022

This is the home page for week 44+45 of the "Bioinformatics in practice" course, Faroe Islands 2022. These five days are taught by Henrik Nielsen and Bent Petersen.

Wednesday November 2

Morning: Introduction, plain text files and taxonomy databases

Lectures:

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

Software for installation:

• Java runtime engine is needed for running some of the software we use in the course, including jEdit (see below). Download from here: https://www.oracle.com/java/technologies/downloads/#java17 (choose java 17, not 18 or 19, and select your type of computer) or from here: https://adoptium.net/ (choose Temurin JDK 17).
  • NOTE: Do NOT download java from https://java.com/ — that will give you Oracle java 8, which is NOT good enough for jEdit anymore. jEdit version 5.6 and later needs java 11 or higher which is available from the above links (and from a few other places).
  • IMPORTANT TIP for Windows users: You need to enable the sub-feature named "set JAVA_HOME variable" when installing Temurin JDK.
• jEdit: http://jedit.org/
  • NOTE: The jEdit developers have not signed the installation package, therefore both Windows and MacOS X will complain when you first attempt to install it, and you have to insist that it is OK to run the program. For Macs, this is a bit complicated, see the instructions in the exercise guide.
  • IMPORTANT TIP for Mac users: If you have an M1 or M2 (ARM) Mac, you should use "Java-based installer" (.jar file) instead of "OS X package" (.dmg file).

Exercises:

• jEdit — Answers
• Taxonomy databases — Answers

Afternoon: GenBank

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

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

Materials:

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

Exercise: Using the GenBank database — Answers

Friday November 4

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 — Answers
• Exercise: The protein database UniProt — Answers

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 — Answers (NB: The section "PyMOL magic" is not part of your curriculum, just a handy tip!)

Monday 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