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.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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== Wednesday November 6 ==
== 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:''' ''[[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/FO2022/22111-ProteinStructure_2022_CBQ-reduced.pdf Protein 3D structure] - Bent''
'''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/ PyMOL]  
'''Software''' for installation: [https://pymol.org/ PyMOL]  
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'''Exercises:'''  
'''Exercises:'''  
* [https://teaching.healthtech.dtu.dk/material/22111/PyMol_tutorial2017_v4.pdf PyMol tutorial] (PDF)
* [[media:PyMol_tutorial2017_v4.pdf|PyMol tutorial]] (PDF)
* [[Protein Structure and Visualization]]
* [[Protein Structure and Visualization]]


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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]] — [[ExPairwiseAlignment-Answers|Answers]]
'''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:''' ''[https://teaching.healthtech.dtu.dk/material/22111/FO2018/Lecture_BLAST_2020.pdf Introduction to BLAST] - Bent''  
'''Lecture:''' ''[[media:Lecture_BLAST_CBQ_BP_2024.pdf|Introduction to BLAST]] - Bent''  


'''Exercise:''' [[Exercise: BLAST]] — [[ExBlast-Answers|Answers]]
'''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]''


== Wednesday November 9 ==
== 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/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] — [https://teaching.healthtech.dtu.dk/material/22111/FO2022/Ex_Logo_ans.pdf Answer]
'''Handout exercise:''' [https://teaching.healthtech.dtu.dk/material/22111/Logo_exercise.pdf How to construct sequence logos]  


'''Exercise:''' [[ExSeqLogos|DNA and Peptide LOGOs]] — [[ExSeqLogosAnswers|Answers]]
'''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/FO2024/PSI-BLAST_FO2024.pdf PSI-BLAST] - Bent''  


'''Exercise:''' [[ExPSIBLAST|PSI-BLAST]] — [[ExPSIBLAST_answer|Answers]]
'''Exercise:''' [[ExPSIBLAST|PSI-BLAST]]


== Friday November 11 ==
== 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 (English version)|Multiple Alignments]] — [[ExMulAlign-Answers-English|Answers]]
'''Exercise:''' [[Exercise: Multiple Alignments (Seaview version)|Multiple Alignments]]


=== Afternoon: Phylogenetic trees ===  
=== Afternoon: Phylogenetic trees ===  
'''Lecture:''' ''[https://teaching.healthtech.dtu.dk/material/22111/FO2022/Gorm_phylogeny_newbackground_rwe_version.pdf Phylogenetic trees] - Bent''
'''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]


'''Software for installation:''' [https://github.com/rambaut/figtree/releases FigTree tree-viewer]
'''Exercise:''' [[Exercise: Phylogeny (Seaview version)|Phylogeny]]
:'''IMPORTANT NOTE''' for Windows users: Download the <tt>.zip</tt> file (FigTree.v1.4.4.zip) and unpack it. Then, go to the "lib" subfolder and double-click the <tt>.jar</tt> file. The <tt>.exe</tt> file may not work.
 
'''Exercise:''' [[Exercise: Phylogeny]] — [[Exercise:_Phylogeny-Answers|Answers]]

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:

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

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