Bioinformatics in practice, Faroe Islands 2024: Difference between revisions

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'''Lecture:''' ''[https://teaching.healthtech.dtu.dk/material/22111/FO2022/Lecture_GenBank_F22_HN.pdf Biological information, DNA, sequencing, and GenBank] - Henrik''  
'''Lecture:''' ''[https://teaching.healthtech.dtu.dk/material/22111/FO2022/Lecture_GenBank_F22_HN.pdf Biological information, DNA, sequencing, and GenBank] - Henrik''  


'''Handout exercise:''' [https://teaching.healthtech.dtu.dk/material/22111/HandoutEx_BaseCalling_Simple.pdf‎ "Base-calling"] (PDF) / [https://teaching.healthtech.dtu.dk/material/22111/BaseCalling_on_screen_version.pdf On-screen version] (PDF)
'''Handout exercise:''' "Base-calling" — [https://teaching.healthtech.dtu.dk/material/22111/HandoutEx_BaseCalling_Simple.pdf Print version] (PDF) / [https://teaching.healthtech.dtu.dk/material/22111/BaseCalling_on_screen_version.pdf On-screen version] (PDF)


'''Materials:'''  
'''Materials:'''  
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'''Materials:''' RevTrans (article, [https://teaching.healthtech.dtu.dk/material/22111/FO2022/RevTrans.pdf PDF])
'''Materials:''' RevTrans (article, [https://teaching.healthtech.dtu.dk/material/22111/FO2022/RevTrans.pdf PDF])


'''Exercise:''' [[Exercise: Multiple Alignments (English version)|Multiple Alignments]]  
'''Exercise:''' [[Exercise: Multiple Alignments (Seaview version)|Multiple Alignments]]


=== Afternoon: Phylogenetic trees ===  
=== Afternoon: Phylogenetic trees ===  
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'''Handout exercise:''' [https://teaching.healthtech.dtu.dk/material/22111/FO2022/handout_distance.pdf Reconstruction of distance tree]
'''Handout exercise:''' [https://teaching.healthtech.dtu.dk/material/22111/FO2022/handout_distance.pdf Reconstruction of distance tree]


'''Exercise:''' [[Exercise: Phylogeny]]
'''Exercise:''' [[Exercise: Phylogeny (Seaview version)|Phylogeny]]

Latest revision as of 13:24, 24 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:

Exercises:

Afternoon: GenBank

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

Handout exercise: "Base-calling" — Print version (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:

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:

Thursday November 7

Morning: Pairwise alignment

Lecture: Pairwise alignment - Henrik

Handout exercise: Alignment scores

Exercise: Pairwise alignment

Wrap-up: Pairwise alignment revisited

Afternoon: Sequence database searching with BLAST

Lecture: Introduction to BLAST - Bent

Exercise: Exercise: BLAST

Wrap-up: BLASTN vs BLASTP

Monday November 11

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

Exercise: DNA and Peptide LOGOs

Afternoon: Profile searching with PSI-BLAST

Lecture: PSI-BLAST - Bent

Exercise: PSI-BLAST

Wednesday November 13

Morning: Multiple alignments

Lecture: Multiple Alignments - Henrik

Materials: RevTrans (article, PDF)

Exercise: Multiple Alignments

Afternoon: Phylogenetic trees

Lecture: Phylogenetic trees - Bent

Handout exercise: Reconstruction of distance tree

Exercise: Phylogeny