Bioinformatics in practice, Faroe Islands 2024: Difference between revisions
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=== Morning: Introduction, plain text files and taxonomy databases === | === Morning: Introduction, plain text files and taxonomy databases === | ||
'''Lectures:''' | '''Lectures:''' | ||
* ''[https://teaching.healthtech.dtu.dk/material/22111/FO2022/Intro+bioinformaticsFO22.pdf Introduction to bioinformatics and computers] - Henrik'' | * ''[[Media:Intro+bioinformaticsFO24.pdf|Introduction to bioinformatics and computers]] - Henrik'' | ||
* ''[https://teaching.healthtech.dtu.dk/material/22111/On_evolution_and_sequences_2020.pdf Evolution & taxonomy] - Bent'' | <!-- * ''[https://teaching.healthtech.dtu.dk/material/22111/FO2022/Intro+bioinformaticsFO22.pdf Introduction to bioinformatics and computers] - Henrik'' --> | ||
* ''[[Media:On_evolution_and_sequences_2024.pdf|Evolution & taxonomy]] - Bent'' | |||
<!-- * ''[https://teaching.healthtech.dtu.dk/material/22111/On_evolution_and_sequences_2020.pdf Evolution & taxonomy] - Bent'' --> | |||
'''Exercises:''' | '''Exercises:''' | ||
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=== Afternoon: GenBank === | === Afternoon: GenBank === | ||
'''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'' --> | ||
'''Lecture:''' ''[[media:Lecture_GenBank_2024.pdf|Biological information, DNA, sequencing, and GenBank]] - Henrik'' | |||
'''Handout exercise:''' [https://teaching.healthtech.dtu.dk/material/22111/HandoutEx_BaseCalling_Simple. | '''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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'''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:''' ''[ | '''Lecture:''' ''[[media:Lecture_UniProt_2024.pdf|Proteins: data and databases]] - Henrik'' | ||
'''Materials:''' | '''Materials:''' | ||
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'''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/ | '''Lecture:''' ''[https://teaching.healthtech.dtu.dk/material/22111/FO2024/22111-ProteinStructure_2024_CBQ_BP.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:''' | ||
* [ | * [[media:PyMol_tutorial2017_v4.pdf|PyMol tutorial]] (PDF) | ||
* [[Protein Structure and Visualization]] | * [[Protein Structure and Visualization]] | ||
== | == Thursday November 7 == | ||
=== Morning: Pairwise alignment === | === Morning: Pairwise alignment === | ||
'''Lecture:''' ''[https://teaching.healthtech.dtu.dk/material/22111/FO2018/PairwiseAlignment2.pdf Pairwise alignment] - Henrik'' | '''Lecture:''' ''[https://teaching.healthtech.dtu.dk/material/22111/FO2018/PairwiseAlignment2.pdf Pairwise alignment] - Henrik'' | ||
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'''Handout exercise:''' [https://teaching.healthtech.dtu.dk/material/22111/New_handout_alignscores.pdf Alignment scores] | '''Handout exercise:''' [https://teaching.healthtech.dtu.dk/material/22111/New_handout_alignscores.pdf Alignment scores] | ||
'''Exercise:''' [[ExPairwiseAlignment|Pairwise alignment | '''Exercise:''' [[ExPairwiseAlignment|Pairwise alignment]] | ||
'''Wrap-up:''' ''[https://teaching.healthtech.dtu.dk/material/22111/FO2018/Pairwise_alignment_revisited.pdf Pairwise alignment revisited]'' | '''Wrap-up:''' ''[https://teaching.healthtech.dtu.dk/material/22111/FO2018/Pairwise_alignment_revisited.pdf Pairwise alignment revisited]'' | ||
=== Afternoon: Sequence database searching with BLAST === | === Afternoon: Sequence database searching with BLAST === | ||
'''Lecture:''' ''[ | '''Lecture:''' ''[[media:Lecture_BLAST_CBQ_BP_2024.pdf|Introduction to BLAST]] - Bent'' | ||
'''Exercise:''' [[Exercise: BLAST | '''Exercise:''' [[Exercise: BLAST]] | ||
'''Wrap-up:''' ''[https://teaching.healthtech.dtu.dk/material/22111/FO2018/Blastn_vs_Blastp.2017.pdf BLASTN vs BLASTP]'' | '''Wrap-up:''' ''[https://teaching.healthtech.dtu.dk/material/22111/FO2018/Blastn_vs_Blastp.2017.pdf BLASTN vs BLASTP]'' | ||
== | == Monday November 11 == | ||
=== Morning: Sequence information and logo plots === | === Morning: Sequence information and logo plots === | ||
'''Lecture:''' ''[https://teaching.healthtech.dtu.dk/material/22111/ | '''Lecture:''' ''[https://teaching.healthtech.dtu.dk/material/22111/FO2024/Logos_2024.pdf Sequence information and logo plots] - Henrik'' | ||
'''Materials:''' "''Information theory primer''" ([https://teaching.healthtech.dtu.dk/material/22111/PDF/informationtheory_primer.pdf PDF]) | '''Materials:''' "''Information theory primer''" ([https://teaching.healthtech.dtu.dk/material/22111/PDF/informationtheory_primer.pdf PDF]) | ||
'''Handout exercise:''' [https://teaching.healthtech.dtu.dk/material/22111/Logo_exercise.pdf How to construct sequence logos | '''Handout exercise:''' [https://teaching.healthtech.dtu.dk/material/22111/Logo_exercise.pdf How to construct sequence logos] | ||
'''Exercise:''' [[ExSeqLogos|DNA and Peptide LOGOs | '''Exercise:''' [[ExSeqLogos|DNA and Peptide LOGOs]] | ||
=== Afternoon: Profile searching with PSI-BLAST === | === Afternoon: Profile searching with PSI-BLAST === | ||
'''Lecture:''' ''[https://teaching.healthtech.dtu.dk/material/22111/ | '''Lecture:''' ''[https://teaching.healthtech.dtu.dk/material/22111/FO2024/PSI-BLAST_FO2024.pdf PSI-BLAST] - Bent'' | ||
'''Exercise:''' [[ExPSIBLAST|PSI-BLAST | '''Exercise:''' [[ExPSIBLAST|PSI-BLAST]] | ||
== | == Wednesday November 13 == | ||
=== Morning: Multiple alignments === | === Morning: Multiple alignments === | ||
'''Lecture:''' ''[https://teaching.healthtech.dtu.dk/material/22111/FO2018/hnielsen_mulalign.pdf Multiple Alignments] - Henrik'' | '''Lecture:''' ''[https://teaching.healthtech.dtu.dk/material/22111/FO2018/hnielsen_mulalign.pdf Multiple Alignments] - Henrik'' | ||
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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 ( | '''Exercise:''' [[Exercise: Multiple Alignments (Seaview version)|Multiple Alignments]] | ||
=== Afternoon: Phylogenetic trees === | === Afternoon: Phylogenetic trees === | ||
'''Lecture:''' ''[ | '''Lecture:''' ''[[media:gorm_phylogeny_newbackground_rwe_BP.pdf|Phylogenetic trees]] - Bent'' | ||
'''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 (Seaview version)|Phylogeny]] | |||
'''Exercise:''' [[Exercise: Phylogeny | |||
Latest revision as of 12:38, 13 November 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" — 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:
- 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:
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