Bioinformatics in practice, Faroe Islands 2024: Difference between revisions
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'''Exercise:''' [[ExGenbank-new|Using the GenBank database]] | '''Exercise:''' [[ExGenbank-new|Using the GenBank database]] | ||
== | == Wednesday November 6 == | ||
=== Morning: Translation and UniProt === | === Morning: Translation and UniProt === | ||
'''Lecture:''' ''[https://teaching.healthtech.dtu.dk/material/22111/FO2022/Lecture_UniProt_2022.pdf Proteins: data and databases] - Henrik'' | '''Lecture:''' ''[https://teaching.healthtech.dtu.dk/material/22111/FO2022/Lecture_UniProt_2022.pdf Proteins: data and databases] - Henrik'' | ||
| Line 33: | Line 33: | ||
'''Exercises:''' | '''Exercises:''' | ||
* [[Exercise: Translation - Virtual Ribosome | * [[Exercise: Translation - Virtual Ribosome]] | ||
* [[Exercise: The protein database UniProt | * [[Exercise: The protein database UniProt]] | ||
=== Afternoon: Protein structure, PDB & PyMOL === | === Afternoon: Protein structure, PDB & PyMOL === | ||
'''Lecture:''' ''[https://teaching.healthtech.dtu.dk/material/22111/FO2022/22111-ProteinStructure_2022_CBQ-reduced.pdf Protein 3D structure] - Bent'' | '''Lecture:''' ''[https://teaching.healthtech.dtu.dk/material/22111/FO2022/22111-ProteinStructure_2022_CBQ-reduced.pdf Protein 3D structure] - Bent'' | ||
'''Software''' for installation: [https://pymol.org | '''Software''' for installation: [https://pymol.org/ PyMOL] | ||
: '''Note:''' you will need a license file which we will provide via Zoom. | : '''Note:''' you will need a license file which we will provide via Zoom. | ||
'''Exercises:''' | '''Exercises:''' | ||
* [https://teaching.healthtech.dtu.dk/material/22111/PyMol_tutorial2017_v4.pdf PyMol tutorial] (PDF) | * [https://teaching.healthtech.dtu.dk/material/22111/PyMol_tutorial2017_v4.pdf PyMol tutorial] (PDF) | ||
* [[Protein Structure and Visualization]] | * [[Protein Structure and Visualization]] | ||
== Monday November 7 == | == Monday November 7 == | ||
Revision as of 15:38, 13 October 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:
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
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:
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:
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