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:
Afternoon: GenBank
Lecture: Biological information, DNA, sequencing, and GenBank - Henrik
Handout exercise: "Base-calling" (PDF) / On-screen version (PDF)
Materials:
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:
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
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