Bioinformatics in practice, Faroe Islands 2024: Difference between revisions

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== Wednesday November 2 ==
== Monday November 4 ==
=== 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''
'''Software for installation:'''
<!-- * ''[https://teaching.healthtech.dtu.dk/material/22111/On_evolution_and_sequences_2020.pdf Evolution & taxonomy] - Bent'' -->
<!-- * java: https://java.com/en/ -->
* '''Java''' runtime engine is needed for running some of the software we use in the course, including jEdit (see below). Download from here: https://www.oracle.com/java/technologies/downloads/#java17 (choose java 17, not 18 or 19, and select your type of computer) '''or''' from here: https://adoptium.net/ (choose Temurin JDK 17).
** '''NOTE:''' Do NOT download java from https://java.com/ — that will give you Oracle java 8, which is NOT good enough for jEdit anymore. jEdit version 5.6 and later needs java 11 or higher which is available from the above links (and from a few other places).
** '''IMPORTANT TIP''' for Windows users: You need to enable the sub-feature named "set JAVA_HOME variable" when installing Temurin JDK.
* jEdit: http://jedit.org/
** '''NOTE:''' The jEdit developers have not signed the installation package, therefore both Windows and MacOS X will complain when you first attempt to install it, and you have to insist that it is OK to run the program. For Macs, this is a bit complicated, see the instructions in [[ExJEdit#Download_and_Install_jEdit|the exercise guide]].
** '''IMPORTANT TIP''' for Mac users: If you have an M1 or M2 (ARM) Mac, you should use "Java-based installer" (.jar file) instead of "OS X package" (.dmg file).


'''Exercises:'''  
'''Exercises:'''  
* [[ExJEdit|jEdit]] — [[ExJEdit-Answers|Answers]]
* [[Plain text files and Geany]]
* [[Taxonomy databases]] — [[ExTaxonomy-Answers|Answers]]
* [[Taxonomy databases]]


=== 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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* [https://teaching.healthtech.dtu.dk/material/22111/GeneStructure.pdf Eukaryotic gene structure overview] (PDF)
* [https://teaching.healthtech.dtu.dk/material/22111/GeneStructure.pdf Eukaryotic gene structure overview] (PDF)


'''Exercise:''' [[ExGenbank-new|Using the GenBank database]] — [[ExGenbank-new-answers|Answers]]
'''Exercise:''' [[ExGenbank-new|Using the GenBank database]]


== Friday November 4 ==
== 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]] — [[ExTranslation-answers|Answers]]
* [[Exercise: Translation - Virtual Ribosome]]  
* [[Exercise: The protein database UniProt]] — [[ExUniProt-answers|Answers]]
* [[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/2/ PyMOL]  
'''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)
* [[media:PyMol_tutorial2017_v4.pdf|PyMol tutorial]] (PDF)
* [[Protein Structure and Visualization]] — [[Protein_Structure_and_Visualization_Answers|Answers]] (NB: The section "PyMOL magic" is ''not'' part of your curriculum, just a handy tip!)
* [[Protein Structure and Visualization]]


== Monday November 7 ==
== 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]] — [[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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