Bioinformatics in practice, Faroe Islands 2022 - Revision history

Henni at 14:36, 3 November 2024

2024-11-03T14:36:58Z

← Older revision		Revision as of 16:36, 3 November 2024
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	'''Exercises:'''		'''Exercises:'''
	* [[ExJEdit\|jEdit]] — [[ExJEdit-Answers\|Answers]]		* [[ExJEdit\|jEdit]] <!-- — [[ExJEdit-Answers\|Answers]] -->
	* [[Taxonomy databases]] — [[ExTaxonomy-Answers\|Answers]]		* [[Taxonomy databases]] <!-- — [[ExTaxonomy-Answers\|Answers]] -->

	=== Afternoon: GenBank ===		=== Afternoon: GenBank ===
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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]] <!-- — [[ExGenbank-new-answers\|Answers]] -->

	== Friday November 4 ==		== Friday November 4 ==
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	'''Exercises:'''		'''Exercises:'''
	* [[Exercise: Translation - Virtual Ribosome]] — [[ExTranslation-answers\|Answers]]		* [[Exercise: Translation - Virtual Ribosome]] <!-- — [[ExTranslation-answers\|Answers]] -->
	* [[Exercise: The protein database UniProt]] — [[ExUniProt-answers\|Answers]]		* [[Exercise: The protein database UniProt]] <!-- — [[ExUniProt-answers\|Answers]] -->

	=== Afternoon: Protein structure, PDB & PyMOL ===		=== Afternoon: Protein structure, PDB & PyMOL ===
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	'''Exercises:'''		'''Exercises:'''
	* [https://teaching.healthtech.dtu.dk/material/22111/PyMol_tutorial2017_v4.pdf PyMol tutorial] (PDF)		* [https://teaching.healthtech.dtu.dk/material/22111/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]] <!-- — [[Protein_Structure_and_Visualization_Answers\|Answers]] (NB: The section "PyMOL magic" is ''not'' part of your curriculum, just a handy tip!) -->

	== Monday November 7 ==		== Monday November 7 ==
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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]] <!-- — [[ExPairwiseAlignment-Answers\|Answers]] -->

	'''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]''
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	'''Lecture:''' ''[https://teaching.healthtech.dtu.dk/material/22111/FO2018/Lecture_BLAST_2020.pdf Introduction to BLAST] - Bent''		'''Lecture:''' ''[https://teaching.healthtech.dtu.dk/material/22111/FO2018/Lecture_BLAST_2020.pdf Introduction to BLAST] - Bent''

	'''Exercise:''' [[Exercise: BLAST]] — [[ExBlast-Answers\|Answers]]		'''Exercise:''' [[Exercise: BLAST]] <!-- — [[ExBlast-Answers\|Answers]] -->

	'''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]''
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	'''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] — [https://teaching.healthtech.dtu.dk/material/22111/FO2022/Ex_Logo_ans.pdf Answer]

	'''Exercise:''' [[ExSeqLogos\|DNA and Peptide LOGOs]] — [[ExSeqLogosAnswers\|Answers]]		'''Exercise:''' [[ExSeqLogos\|DNA and Peptide LOGOs]] <!-- — [[ExSeqLogosAnswers\|Answers]] -->

	=== 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]] — [[ExPSIBLAST_answer\|Answers]]		'''Exercise:''' [[ExPSIBLAST\|PSI-BLAST]] <!-- — [[ExPSIBLAST_answer\|Answers]] -->

	== Friday November 11 ==		== Friday November 11 ==
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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 (English version)\|Multiple Alignments]] <!-- — [[ExMulAlign-Answers-English\|Answers]] -->

	=== Afternoon: Phylogenetic trees ===		=== Afternoon: Phylogenetic trees ===
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	:'''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.		:'''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]]		'''Exercise:''' [[Exercise: Phylogeny]] <!-- — [[Exercise:_Phylogeny-Answers\|Answers]] -->

Henni: /* Morning: Introduction, plain text files and taxonomy databases */

2024-08-29T16:05:44Z

Morning: Introduction, plain text files and taxonomy databases

← Older revision		Revision as of 18:05, 29 August 2024
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	'''Exercises:'''		'''Exercises:'''
	* [[ExJEdit\|jEdit]] — [[ExJEdit-Answers\|Answers]]		* [[ExJEdit\|jEdit]] — [[ExJEdit-Answers\|Answers]]
	* [[~~ExTaxonomy\|~~Taxonomy databases]] — [[ExTaxonomy-Answers\|Answers]]		* [[Taxonomy databases]] — [[ExTaxonomy-Answers\|Answers]]

	=== Afternoon: GenBank ===		=== Afternoon: GenBank ===

WikiSysop: /* Afternoon: Phylogenetic trees */

2024-03-15T12:07:31Z

Afternoon: Phylogenetic trees

← Older revision		Revision as of 14:07, 15 March 2024
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	=== Afternoon: Phylogenetic trees ===		=== Afternoon: Phylogenetic trees ===
	'''Lecture:''' ''[https://teaching.healthtech.dtu.dk/material/22111/~~F02022~~/Gorm_phylogeny_newbackground_rwe_version.pdf Phylogenetic trees] - Bent''		'''Lecture:''' ''[https://teaching.healthtech.dtu.dk/material/22111/FO2022/Gorm_phylogeny_newbackground_rwe_version.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]

WikiSysop: /* Afternoon: GenBank */

2024-03-15T12:05:12Z

Afternoon: GenBank

← Older revision		Revision as of 14:05, 15 March 2024
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	'''Materials:'''		'''Materials:'''
	* [https://teaching.healthtech.dtu.dk/material/22111/GenBank+FASTA_handout_revised.pdf GenBank + FASTA format] (PDF)		* [https://teaching.healthtech.dtu.dk/material/22111/GenBank+FASTA_handout_revised.pdf GenBank + FASTA format] (PDF)
	* [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]] — [[ExGenbank-new-answers\|Answers]]

WikiSysop at 12:03, 15 March 2024

2024-03-15T12:03:38Z

WikiSysop: Created page with "This is the home page for week 44+45 of the "Bioinformatics in practice" course, Faroe Islands 2022. These five days are taught by [http://www.dtu.dk/service/telefonbog/person?id=25617&cpid=214126&tab=2&qt=dtupublicationquery Henrik Nielsen] and [https://globe.ku.dk/staff-list/hologenomics/?id=271131&vis=medarbejder Bent Petersen]. == Wednesday November 2 == === Morning: Introduction, plain text files and taxonomy databases === '''Lectures:''' * ''[https://teaching.he..."

2024-03-15T11:50:38Z

Created page with "This is the home page for week 44+45 of the "Bioinformatics in practice" course, Faroe Islands 2022. These five days are taught by [http://www.dtu.dk/service/telefonbog/person?id=25617&cpid=214126&tab=2&qt=dtupublicationquery Henrik Nielsen] and [https://globe.ku.dk/staff-list/hologenomics/?id=271131&vis=medarbejder Bent Petersen]. == Wednesday November 2 == === Morning: Introduction, plain text files and taxonomy databases === '''Lectures:''' * ''[https://teaching.he..."

New page

This is the home page for week 44+45 of the "Bioinformatics in practice" course, Faroe Islands 2022. These five days are taught by [http://www.dtu.dk/service/telefonbog/person?id=25617&cpid=214126&tab=2&qt=dtupublicationquery Henrik Nielsen] and [https://globe.ku.dk/staff-list/hologenomics/?id=271131&vis=medarbejder Bent Petersen].

== Wednesday November 2 ==
=== Morning: Introduction, plain text files and taxonomy databases ===
'''Lectures:'''
* ''[https://teaching.healthtech.dtu.dk/material/36611/FO2022/Intro+bioinformaticsFO22.pdf Introduction to bioinformatics and computers] - Henrik''
* ''[https://teaching.healthtech.dtu.dk/22111/images/c/c1/On_evolution_and_sequences_2020.pdf Evolution & taxonomy] - Bent''

'''Software for installation:'''

* '''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:'''
* [[ExJEdit|jEdit]] — [[ExJEdit-Answers|Answers]]
* [[ExTaxonomy|Taxonomy databases]] — [[ExTaxonomy-Answers|Answers]]

=== Afternoon: GenBank ===
'''Lecture:''' ''[https://teaching.healthtech.dtu.dk/material/36611/FO2022/Lecture_GenBank_F22_HN.pdf Biological information, DNA, sequencing, and GenBank] - Henrik''

'''Handout exercise:''' [[Media:HandoutEx_BaseCalling_Simple.pdf‎|"Base-calling"]] (PDF) / [[Media:BaseCalling_on_screen_version.pdf|On-screen version]] (PDF)

'''Materials:'''
* [[Media:GenBank+FASTA_handout_revised.pdf|GenBank + FASTA format]] (PDF)
* [[Media:GeneStructure.pdf|Eukaryotic gene structure overview]] (PDF)

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

== Friday November 4 ==
=== Morning: Translation and UniProt ===
'''Lecture:''' ''[https://teaching.healthtech.dtu.dk/material/36611/FO2022/Lecture_UniProt_2022.pdf Proteins: data and databases] - Henrik''

'''Materials:'''
* [[Media:VirtualRibosome.pdf|Virtual Ribosome]] — software article (PDF)
* [http://www.cbs.dtu.dk/dtucourse/27611spring2011/PDF/protein_handout.pdf Proteins, levels of structure] (PDF)
* [[Media:GeneStructure.pdf|Eukaryotic gene structure overview]] (PDF)

'''Exercises:'''
* [[Exercise: Translation - Virtual Ribosome]] — [[ExTranslation-answers|Answers]]
* [[Exercise: The protein database UniProt]] — [[ExUniProt-answers|Answers]]

=== Afternoon: Protein structure, PDB & PyMOL ===
'''Lecture:''' ''[https://teaching.healthtech.dtu.dk/material/36611/FO2022/22111-ProteinStructure_2022_CBQ-reduced.pdf Protein 3D structure] - Bent''

'''Software''' for installation: [https://pymol.org/2/ PyMOL]
: '''Note:''' you will need a license file which we will provide via Zoom.

'''Exercises:'''
* [[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!)

== Monday November 7 ==
=== Morning: Pairwise alignment ===
'''Lecture:''' ''[http://teaching.healthtech.dtu.dk/material/36611/FO2018/PairwiseAlignment2.pdf Pairwise alignment] - Henrik''

'''Handout exercise:''' [[Media:New_handout_alignscores.pdf|Alignment scores]]

'''Exercise:''' [[ExPairwiseAlignment|Pairwise alignment]] — [[ExPairwiseAlignment-Answers|Answers]]

'''Wrap-up:''' ''[http://teaching.healthtech.dtu.dk/material/36611/FO2018/Pairwise_alignment_revisited.pdf Pairwise alignment revisited]''

=== Afternoon: Sequence database searching with BLAST ===
'''Lecture:''' ''[http://teaching.healthtech.dtu.dk/material/36611/FO2018/Lecture_BLAST_2020.pdf Introduction to BLAST] - Bent''

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

'''Wrap-up:''' ''[http://teaching.healthtech.dtu.dk/material/36611/FO2018/Blastn_vs_Blastp.2017.pdf BLASTN vs BLASTP]''

== Wednesday November 9 ==
=== Morning: Sequence information and logo plots ===
'''Lecture:''' ''[https://teaching.healthtech.dtu.dk/material/36611/FO2022/Logos_2022.pdf Sequence information and logo plots] - Henrik''

'''Materials:''' "''Information theory primer''" ([https://teaching.healthtech.dtu.dk/material/36611/PDF/informationtheory_primer.pdf PDF])

'''Handout exercise:''' [[Media:logo_exercise.pdf|How to construct sequence logos]] — [https://teaching.healthtech.dtu.dk/material/36611/FO2022/Ex_Logo_ans.pdf Answer]

'''Exercise:''' [[ExSeqLogos|DNA and Peptide LOGOs]] — [[ExSeqLogosAnswers|Answers]]

=== Afternoon: Profile searching with PSI-BLAST ===
'''Lecture:''' ''[https://teaching.healthtech.dtu.dk/material/36611/FO2022/PSI-BLAST_FO2022.pdf PSI-BLAST] - Bent''

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

== Friday November 11 ==
=== Morning: Multiple alignments ===
'''Lecture:''' ''[http://teaching.healthtech.dtu.dk/material/36611/FO2018/hnielsen_mulalign.pdf Multiple Alignments] - Henrik''

'''Materials:''' RevTrans (article, [https://teaching.healthtech.dtu.dk/material/36611/FO2022/RevTrans.pdf PDF])

'''Exercise:''' [[Exercise: Multiple Alignments (English version)|Multiple Alignments]] — [[ExMulAlign-Answers-English|Answers]]

=== Afternoon: Phylogenetic trees ===
'''Lecture:''' ''[https://teaching.healthtech.dtu.dk/22111/images/5/55/Gorm_phylogeny_newbackground_rwe_version.pdf Phylogenetic trees] - Bent''

'''Handout exercise:''' [https://teaching.healthtech.dtu.dk/material/36611/FO2022/handout_distance.pdf Reconstruction of distance tree]

'''Software for installation:''' [https://github.com/rambaut/figtree/releases FigTree tree-viewer]
:'''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]]

← Older revision		Revision as of 14:03, 15 March 2024
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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/~~36611~~/FO2022/Intro+bioinformaticsFO22.pdf Introduction to bioinformatics and computers] - Henrik''		* ''[https://teaching.healthtech.dtu.dk/material/22111/FO2022/Intro+bioinformaticsFO22.pdf Introduction to bioinformatics and computers] - Henrik''
	* ''[https://teaching.healthtech.dtu.dk/22111~~/images/c/c1~~/On_evolution_and_sequences_2020.pdf Evolution & taxonomy] - Bent''		* ''[https://teaching.healthtech.dtu.dk/material/22111/On_evolution_and_sequences_2020.pdf Evolution & taxonomy] - Bent''

	'''Software for installation:'''		'''Software for installation:'''
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	=== Afternoon: GenBank ===		=== Afternoon: GenBank ===
	'''Lecture:''' ''[https://teaching.healthtech.dtu.dk/material/~~36611~~/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:''' [~~[Media~~:HandoutEx_BaseCalling_Simple.pdf‎\|"Base-calling"]] (PDF) / [~~[Media~~:BaseCalling_on_screen_version.pdf\|On-screen version]] (PDF)		'''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)

	'''Materials:'''		'''Materials:'''
	* [~~[Media~~:GenBank+FASTA_handout_revised.pdf\|GenBank + FASTA format]] (PDF)		* [https://teaching.healthtech.dtu.dk/material/22111/GenBank+FASTA_handout_revised.pdf GenBank + FASTA format] (PDF)
	* [~~[Media~~: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]] — [[ExGenbank-new-answers\|Answers]]
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	== Friday November 4 ==		== Friday November 4 ==
	=== Morning: Translation and UniProt ===		=== Morning: Translation and UniProt ===
	'''Lecture:''' ''[https://teaching.healthtech.dtu.dk/material/~~36611~~/FO2022/Lecture_UniProt_2022.pdf Proteins: data and databases] - Henrik''		'''Lecture:''' ''[https://teaching.healthtech.dtu.dk/material/22111/FO2022/Lecture_UniProt_2022.pdf Proteins: data and databases] - Henrik''

	'''Materials:'''		'''Materials:'''
	* [~~[Media~~:VirtualRibosome.pdf\|Virtual Ribosome]] — software article (PDF)		* [https://teaching.healthtech.dtu.dk/material/22111/VirtualRibosome.pdf Virtual Ribosome] — software article (PDF)
	* [~~http~~://~~www~~.~~cbs~~.dtu.dk/~~dtucourse~~/~~27611spring2011~~/PDF/protein_handout.pdf Proteins, levels of structure] (PDF)		* [https://teaching.healthtech.dtu.dk/material/22111/PDF/protein_handout.pdf Proteins, levels of structure] (PDF)
	* [~~[Media~~:GeneStructure.pdf\|Eukaryotic gene structure overview]] (PDF)		* [https://teaching.healthtech.dtu.dk/material/22111/GeneStructure.pdf Eukaryotic gene structure overview] (PDF)

	'''Exercises:'''		'''Exercises:'''
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	=== Afternoon: Protein structure, PDB & PyMOL ===		=== Afternoon: Protein structure, PDB & PyMOL ===
	'''Lecture:''' ''[https://teaching.healthtech.dtu.dk/material/~~36611~~/FO2022/22111-ProteinStructure_2022_CBQ-reduced.pdf Protein 3D structure] - Bent''		'''Lecture:''' ''[https://teaching.healthtech.dtu.dk/material/22111/FO2022/22111-ProteinStructure_2022_CBQ-reduced.pdf Protein 3D structure] - Bent''

	'''Software''' for installation: [https://pymol.org/2/ PyMOL]		'''Software''' for installation: [https://pymol.org/2/ PyMOL]
Line 52:		Line 52:

	'''Exercises:'''		'''Exercises:'''
	* [~~[Media~~:PyMol_tutorial2017_v4.pdf\|PyMol tutorial]] (PDF)		* [https://teaching.healthtech.dtu.dk/material/22111/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]] — [[Protein_Structure_and_Visualization_Answers\|Answers]] (NB: The section "PyMOL magic" is ''not'' part of your curriculum, just a handy tip!)

	== Monday November 7 ==		== Monday November 7 ==
	=== Morning: Pairwise alignment ===		=== Morning: Pairwise alignment ===
	'''Lecture:''' ''[~~http~~://teaching.healthtech.dtu.dk/material/~~36611~~/FO2018/PairwiseAlignment2.pdf Pairwise alignment] - Henrik''		'''Lecture:''' ''[https://teaching.healthtech.dtu.dk/material/22111/FO2018/PairwiseAlignment2.pdf Pairwise alignment] - Henrik''

	'''Handout exercise:''' [~~[Media~~: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]] — [[ExPairwiseAlignment-Answers\|Answers]]

	'''Wrap-up:''' ''[~~http~~://teaching.healthtech.dtu.dk/material/~~36611~~/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:''' ''[~~http~~://teaching.healthtech.dtu.dk/material/~~36611~~/FO2018/Lecture_BLAST_2020.pdf Introduction to BLAST] - Bent''		'''Lecture:''' ''[https://teaching.healthtech.dtu.dk/material/22111/FO2018/Lecture_BLAST_2020.pdf Introduction to BLAST] - Bent''

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

	'''Wrap-up:''' ''[~~http~~://teaching.healthtech.dtu.dk/material/~~36611~~/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 ==		== Wednesday November 9 ==
	=== Morning: Sequence information and logo plots ===		=== Morning: Sequence information and logo plots ===
	'''Lecture:''' ''[https://teaching.healthtech.dtu.dk/material/~~36611~~/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''

	'''Materials:''' "''Information theory primer''" ([https://teaching.healthtech.dtu.dk/material/~~36611~~/PDF/informationtheory_primer.pdf PDF])		'''Materials:''' "''Information theory primer''" ([https://teaching.healthtech.dtu.dk/material/22111/PDF/informationtheory_primer.pdf PDF])

	'''Handout exercise:''' [~~[Media~~:~~logo_exercise~~.pdf\|How to construct sequence logos]] — [https://teaching.healthtech.dtu.dk/material/~~36611~~/FO2022/Ex_Logo_ans.pdf Answer]		'''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]

	'''Exercise:''' [[ExSeqLogos\|DNA and Peptide LOGOs]] — [[ExSeqLogosAnswers\|Answers]]		'''Exercise:''' [[ExSeqLogos\|DNA and Peptide LOGOs]] — [[ExSeqLogosAnswers\|Answers]]

	=== Afternoon: Profile searching with PSI-BLAST ===		=== Afternoon: Profile searching with PSI-BLAST ===
	'''Lecture:''' ''[https://teaching.healthtech.dtu.dk/material/~~36611~~/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]] — [[ExPSIBLAST_answer\|Answers]]		'''Exercise:''' [[ExPSIBLAST\|PSI-BLAST]] — [[ExPSIBLAST_answer\|Answers]]
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	== Friday November 11 ==		== Friday November 11 ==
	=== Morning: Multiple alignments ===		=== Morning: Multiple alignments ===
	'''Lecture:''' ''[~~http~~://teaching.healthtech.dtu.dk/material/~~36611~~/FO2018/hnielsen_mulalign.pdf Multiple Alignments] - Henrik''		'''Lecture:''' ''[https://teaching.healthtech.dtu.dk/material/22111/FO2018/hnielsen_mulalign.pdf Multiple Alignments] - Henrik''

	'''Materials:''' RevTrans (article, [https://teaching.healthtech.dtu.dk/material/~~36611~~/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 (English version)\|Multiple Alignments]] — [[ExMulAlign-Answers-English\|Answers]]

	=== Afternoon: Phylogenetic trees ===		=== Afternoon: Phylogenetic trees ===
	'''Lecture:''' ''[https://teaching.healthtech.dtu.dk/22111/~~images/5/55~~/Gorm_phylogeny_newbackground_rwe_version.pdf Phylogenetic trees] - Bent''		'''Lecture:''' ''[https://teaching.healthtech.dtu.dk/material/22111/F02022/Gorm_phylogeny_newbackground_rwe_version.pdf Phylogenetic trees] - Bent''

	'''Handout exercise:''' [https://teaching.healthtech.dtu.dk/material/~~36611~~/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]		'''Software for installation:''' [https://github.com/rambaut/figtree/releases FigTree tree-viewer]