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. | '''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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'''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/FO2022/Logos_2022.pdf Sequence information and logo plots] - Henrik'' | '''Lecture:''' ''[https://teaching.healthtech.dtu.dk/material/22111/FO2022/Logos_2022.pdf Sequence information and logo plots] - Henrik'' | ||
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'''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/FO2022/PSI-BLAST_FO2022.pdf PSI-BLAST] - Bent'' | '''Lecture:''' ''[https://teaching.healthtech.dtu.dk/material/22111/FO2022/PSI-BLAST_FO2022.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 === | ||
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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 (Seaview version)|Phylogeny]] | |||
'''Exercise:''' [[Exercise: 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:
- 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