22111:Course plan autumn 2023 - Revision history

WikiSysop: /* Thursday Dec 14 */

2024-03-15T10:41:39Z

Thursday Dec 14

← Older revision		Revision as of 12:41, 15 March 2024
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	'''Winter exam 2023:''' Go to https://eksamen.dtu.dk/ and find 22111.		'''Winter exam 2023:''' Go to https://eksamen.dtu.dk/ and find 22111.

	[~~[Media~~:Vejledning-til-digital-eksamen-DE-~~DKENG_0322~~.pdf\|Here is a guide]] to the Digital Exam interface (in Danish and English).		[https://teaching.healthtech.dtu.dk/material/22111/Vejledning-til-digital-eksamen-DE-DK-ENG-revideret-2023-.pdf Here is a guide] to the Digital Exam interface (in Danish and English).

	The assignment will be accessible from '''15:00''' on Thursday Dec 14.		The assignment will be accessible from '''15:00''' on Thursday Dec 14.

WikiSysop: /* Tuesday Nov 21 — Phylogenetic trees */

2024-03-15T10:20:07Z

Tuesday Nov 21 — Phylogenetic trees

← Older revision		Revision as of 12:20, 15 March 2024
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	:# ''Introduction to Tree Building'', PDF on Learn <!-- XXX WHERE? → Slides etc → Lecture12 -->		:# ''Introduction to Tree Building'', PDF on Learn <!-- XXX WHERE? → Slides etc → Lecture12 -->
	:# ''[http://evolution.berkeley.edu/evolibrary/article/phylogenetics_01 Evolutionary trees]'' (minus the section "How to reconstruct an evolutionary tree")		:# ''[http://evolution.berkeley.edu/evolibrary/article/phylogenetics_01 Evolutionary trees]'' (minus the section "How to reconstruct an evolutionary tree")
	:# ''Understanding Evolutionary Trees'', [https://teaching.healthtech.dtu.dk/material/~~36611~~/PDF/understanding_evo_trees.pdf PDF].		:# ''Understanding Evolutionary Trees'', [https://teaching.healthtech.dtu.dk/material/22111/PDF/understanding_evo_trees.pdf PDF].
	:'''Slides:''' on DTU Learn.		:'''Slides:''' on DTU Learn.
	:'''Handout''' for lecture: [https://teaching.healthtech.dtu.dk/material/~~36611~~/PDF/handout_distance.pdf Reconstructing a distance tree] <-- ([~~[Media~~:~~handout_distance_answers~~.pdf\|Answer]]) -->		:'''Handout''' for lecture: [https://teaching.healthtech.dtu.dk/material/22111/PDF/handout_distance.pdf Reconstructing a distance tree] <-- ([https://teaching.healthtech.dtu.dk/material/22111/Handout_distance_answers.pdf Answer]) -->
	<!-- :'''Software''' for installation: [https://github.com/rambaut/figtree/releases FigTree tree-viewer]		<!-- :'''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.		::'''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.

WikiSysop: /* Tuesday Oct 31 — Weight matrices and other prediction methods */

2024-03-15T09:50:26Z

Tuesday Oct 31 — Weight matrices and other prediction methods

← Older revision		Revision as of 11:50, 15 March 2024
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	<!--:'''Handouts''' for the lecture: -->		<!--:'''Handouts''' for the lecture: -->
	:'''Exercises:'''		:'''Exercises:'''
	:# [https://teaching.healthtech.dtu.dk/material/22111/Estimationofpseudocounts_new+examples.pdf How to estimate pseudo frequencies] <-- ([https://teaching.healthtech.dtu.dk/~~material22111~~/Estimationofpseudocounts_answer_brief.pdf Answer]) --> '''Note''': If you solve this manually, just select a couple of amino acids from the table. But if you solve it programmatically (python, Excel, other...), fill out the entire table.		:# [https://teaching.healthtech.dtu.dk/material/22111/Estimationofpseudocounts_new+examples.pdf How to estimate pseudo frequencies] <-- ([https://teaching.healthtech.dtu.dk/material/22111/Estimationofpseudocounts_answer_brief.pdf Answer]) --> '''Note''': If you solve this manually, just select a couple of amino acids from the table. But if you solve it programmatically (python, Excel, other...), fill out the entire table.
	:# [[Exercise: Construction of sequence logos and weight matrices\|Construction of weight matrices]] <-- - ([[ExLogo+Matrix-answers\|Answers]]) -->		:# [[Exercise: Construction of sequence logos and weight matrices\|Construction of weight matrices]] <-- - ([[ExLogo+Matrix-answers\|Answers]]) -->
	:'''Link to advanced course: '''		:'''Link to advanced course: '''

WikiSysop: /* Tuesday Oct 31 — Weight matrices and other prediction methods */

2024-03-15T09:49:57Z

Tuesday Oct 31 — Weight matrices and other prediction methods

← Older revision		Revision as of 11:49, 15 March 2024
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	<!--:'''Handouts''' for the lecture: -->		<!--:'''Handouts''' for the lecture: -->
	:'''Exercises:'''		:'''Exercises:'''
	:# [https://teaching.healthtech.dtu.dk/~~material22111~~/Estimationofpseudocounts_new+examples.pdf How to estimate pseudo frequencies] <-- ([https://teaching.healthtech.dtu.dk/material22111/Estimationofpseudocounts_answer_brief.pdf Answer]) --> '''Note''': If you solve this manually, just select a couple of amino acids from the table. But if you solve it programmatically (python, Excel, other...), fill out the entire table.		:# [https://teaching.healthtech.dtu.dk/material/22111/Estimationofpseudocounts_new+examples.pdf How to estimate pseudo frequencies] <-- ([https://teaching.healthtech.dtu.dk/material22111/Estimationofpseudocounts_answer_brief.pdf Answer]) --> '''Note''': If you solve this manually, just select a couple of amino acids from the table. But if you solve it programmatically (python, Excel, other...), fill out the entire table.
	:# [[Exercise: Construction of sequence logos and weight matrices\|Construction of weight matrices]] <-- - ([[ExLogo+Matrix-answers\|Answers]]) -->		:# [[Exercise: Construction of sequence logos and weight matrices\|Construction of weight matrices]] <-- - ([[ExLogo+Matrix-answers\|Answers]]) -->
	:'''Link to advanced course: '''		:'''Link to advanced course: '''

WikiSysop: /* Tuesday Oct 31 — Weight matrices and other prediction methods */

2024-03-15T09:46:32Z

Tuesday Oct 31 — Weight matrices and other prediction methods

← Older revision		Revision as of 11:46, 15 March 2024
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	<!--:'''Handouts''' for the lecture: -->		<!--:'''Handouts''' for the lecture: -->
	:'''Exercises:'''		:'''Exercises:'''
	:# [~~[Media~~:Estimationofpseudocounts_new+examples.pdf\|How to estimate pseudo frequencies]] <-- ([~~[Media~~:Estimationofpseudocounts_answer_brief.pdf\|Answer]]) --> '''Note''': If you solve this manually, just select a couple of amino acids from the table. But if you solve it programmatically (python, Excel, other...), fill out the entire table.		:# [https://teaching.healthtech.dtu.dk/material22111/Estimationofpseudocounts_new+examples.pdf How to estimate pseudo frequencies] <-- ([https://teaching.healthtech.dtu.dk/material22111/Estimationofpseudocounts_answer_brief.pdf Answer]) --> '''Note''': If you solve this manually, just select a couple of amino acids from the table. But if you solve it programmatically (python, Excel, other...), fill out the entire table.
	:# [[Exercise: Construction of sequence logos and weight matrices\|Construction of weight matrices]] <-- - ([[ExLogo+Matrix-answers\|Answers]]) -->		:# [[Exercise: Construction of sequence logos and weight matrices\|Construction of weight matrices]] <-- - ([[ExLogo+Matrix-answers\|Answers]]) -->
	:'''Link to advanced course: '''		:'''Link to advanced course: '''

WikiSysop: /* Tuesday Oct 24 — Sequence information & logo-plots */

2024-03-15T09:24:02Z

Tuesday Oct 24 — Sequence information & logo-plots

← Older revision		Revision as of 11:24, 15 March 2024
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	:'''Curriculum:'''		:'''Curriculum:'''
	:# Pages 68-80 in Immunological Bioinformatics (PDF: on DTU Learn).		:# Pages 68-80 in Immunological Bioinformatics (PDF: on DTU Learn).
	:# Pages 1-8 of "''Information theory primer''" ([https://teaching.healthtech.dtu.dk/material/~~36611~~/PDF/informationtheory_primer.pdf PDF])		:# Pages 1-8 of "''Information theory primer''" ([https://teaching.healthtech.dtu.dk/material/22111/PDF/informationtheory_primer.pdf PDF])
	:#* Read also the appendix on logarithms (especially log<sub>2</sub>) if needed!		:#* Read also the appendix on logarithms (especially log<sub>2</sub>) if needed!
	:'''Slides:''' on DTU Learn.		:'''Slides:''' on DTU Learn.
	:'''Handout''' for the lecture: [~~[Media~~:~~logo_exercise~~.pdf\|How to construct sequence logos]] (PDF)		:'''Handout''' for the lecture: [https://teaching.healthtech.dtu.dk/material/22111/Logo_exercise.pdf How to construct sequence logos] (PDF)
	:'''Exercise:''' [[ExSeqLogos\|DNA and Peptide Logos]] <-- — ([[ExSeqLogosAnswers\|Answers]]) -->		:'''Exercise:''' [[ExSeqLogos\|DNA and Peptide Logos]] <-- — ([[ExSeqLogosAnswers\|Answers]]) -->

WikiSysop: /* Tuesday Oct 3 — Protein structure, PDB & PyMOL */

2024-03-15T09:06:47Z

Tuesday Oct 3 — Protein structure, PDB & PyMOL

← Older revision		Revision as of 11:06, 15 March 2024
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	:'''Link to advanced course:'''		:'''Link to advanced course:'''
	::* [~~http~~://teaching.healthtech.dtu.dk/~~36617~~/index.php/22117_-_Protein_Structure_and_Computational_Biology 22117 Protein Structure and Computational Biology]		::* [https://teaching.healthtech.dtu.dk/22117/index.php/22117_-_Protein_Structure_and_Computational_Biology 22117 Protein Structure and Computational Biology]

	:'''Software''' for installation: [https://pymol.org/2/ PyMOL]		:'''Software''' for installation: [https://pymol.org/2/ PyMOL]
	::'''Note:''' you will need the license file found at DTU Learn under this week's topic. The license is valid for a limited time. If you need PyMOL for educational purposes later in your studies, you can go to https://pymol.org/edu/index.php and register as a student to get your own license file (and if you don't receive an email after registering, write to help@schrodinger.com). However, if you need PyMOL to make figures for a scientific publication, you will have to pay for a license.		::'''Note:''' you will need the license file found at DTU Learn under this week's topic. The license is valid for a limited time. If you need PyMOL for educational purposes later in your studies, you can go to https://pymol.org/edu/index.php and register as a student to get your own license file (and if you don't receive an email after registering, write to help@schrodinger.com). However, if you need PyMOL to make figures for a scientific publication, you will have to pay for a license.
	:'''Exercises:'''		:'''Exercises:'''
	:#[~~[Media~~:PyMol_tutorial2017_v4.pdf\|PyMol tutorial]] (PDF) — basic usage of PyMOL.		:#[https://teaching.healthtech.dtu.dk/material/22111/PyMol_tutorial2017_v4.pdf PyMol tutorial] (PDF) — basic usage of PyMOL.
	:#[[Protein Structure and Visualization]] <-- — ([[Protein_Structure_and_Visualization_Answers\|Answers]]; NB: the last section labelled "PyMOL magic" is NOT curriculum, just a tip!) -->		:#[[Protein Structure and Visualization]] <-- — ([[Protein_Structure_and_Visualization_Answers\|Answers]]; NB: the last section labelled "PyMOL magic" is NOT curriculum, just a tip!) -->
	:'''Extra material:'''		:'''Extra material:'''
	:*[https://doi.org/10.1093/nar/gkac1077 "RCSB Protein Data Bank (RCSB.org): delivery of experimentally-determined PDB structures alongside one million computed structure models of proteins from artificial intelligence/machine learning"] — article from the annual database issue of Nucleic Acids Research, 2023.		:*[https://doi.org/10.1093/nar/gkac1077 "RCSB Protein Data Bank (RCSB.org): delivery of experimentally-determined PDB structures alongside one million computed structure models of proteins from artificial intelligence/machine learning"] — article from the annual database issue of Nucleic Acids Research, 2023.
	:*[[PyMOL]] — some tips and tricks.		:*[[PyMOL]] — some tips and tricks.
	:*[https://teaching.healthtech.dtu.dk/material/~~36611~~/PDF/PyMOL_structure_navigation.pdf PyMOL basics — a small example] (optional extra exercise)		:*[https://teaching.healthtech.dtu.dk/material/22111/PDF/PyMOL_structure_navigation.pdf PyMOL basics — a small example] (optional extra exercise)

	=== Tuesday Oct 10 — Case: Malaria vaccine ===		=== Tuesday Oct 10 — Case: Malaria vaccine ===

WikiSysop at 16:22, 13 March 2024

2024-03-13T16:22:54Z

← Older revision		Revision as of 18:22, 13 March 2024
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	:'''Test of prior knowledge:''' Go to https://evaluering.dtu.dk/, click "Test of prior knowledge" under 22111, and fill out the form (it's anonymous). Spend max. 10 minutes on it.		:'''Test of prior knowledge:''' Go to https://evaluering.dtu.dk/, click "Test of prior knowledge" under 22111, and fill out the form (it's anonymous). Spend max. 10 minutes on it.
	-->		-->
	:'''Exercise:''' [[ExGenbank-new\|Using the GenBank database]] <!-- — ([[ExGenbank-new-answers\|Answers]]) -->		:'''Exercise:''' [[ExGenbank-new\|Using the GenBank database]] <-- — ([[ExGenbank-new-answers\|Answers]]) -->
	:'''Reference material''' for the exercise: [https://teaching.healthtech.dtu.dk/material/22111/GenBank+FASTA_handout_revised.pdf GenBank + FASTA format] [PDF]		:'''Reference material''' for the exercise: [https://teaching.healthtech.dtu.dk/material/22111/GenBank+FASTA_handout_revised.pdf GenBank + FASTA format] [PDF]

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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]]) -->
	:'''Background material''' (supposedly known):		:'''Background material''' (supposedly known):
	:*[https://teaching.healthtech.dtu.dk/material/22111/PDF/protein_handout.pdf Levels of protein structure] [PDF]		:*[https://teaching.healthtech.dtu.dk/material/22111/PDF/protein_handout.pdf Levels of protein structure] [PDF]
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	:'''Handout''' for the lecture: [https://teaching.healthtech.dtu.dk/material/22111/New_handout_alignscores.pdf Alignment scores]		:'''Handout''' for the lecture: [https://teaching.healthtech.dtu.dk/material/22111/New_handout_alignscores.pdf Alignment scores]
	:'''Slides:''' on DTU Learn.		:'''Slides:''' on DTU Learn.
	:'''Exercise:''' [[ExPairwiseAlignment\|Pairwise alignment]] <!-- — ([[ExPairwiseAlignment-AnswersEng\|Answers]]) -->		:'''Exercise:''' [[ExPairwiseAlignment\|Pairwise alignment]] <-- — ([[ExPairwiseAlignment-AnswersEng\|Answers]]) -->

	=== Tuesday Sep 26 — BLAST ===		=== Tuesday Sep 26 — BLAST ===
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	:'''Curriculum:''' section 3.2.5 → 3.3 (i.e. pages 47-52) in Immunological Bioinformatics (PDF: on DTU Learn).		:'''Curriculum:''' section 3.2.5 → 3.3 (i.e. pages 47-52) in Immunological Bioinformatics (PDF: on DTU Learn).
	:'''Slides:''' on DTU Learn.		:'''Slides:''' on DTU Learn.
	:'''Exercise: [[Exercise:_BLAST2\|BLAST]]''' <!-- — ([[ExBlast-Answers\|Answers]]) -->		:'''Exercise: [[Exercise:_BLAST2\|BLAST]]''' <-- — ([[ExBlast-Answers\|Answers]]) -->
	<!--		<!--
	:'''Extra material:'''		:'''Extra material:'''
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	:'''Exercises:'''		:'''Exercises:'''
	:#[[Media:PyMol_tutorial2017_v4.pdf\|PyMol tutorial]] (PDF) — basic usage of PyMOL.		:#[[Media:PyMol_tutorial2017_v4.pdf\|PyMol tutorial]] (PDF) — basic usage of PyMOL.
	:#[[Protein Structure and Visualization]] <!-- — ([[Protein_Structure_and_Visualization_Answers\|Answers]]; NB: the last section labelled "PyMOL magic" is NOT curriculum, just a tip!) -->		:#[[Protein Structure and Visualization]] <-- — ([[Protein_Structure_and_Visualization_Answers\|Answers]]; NB: the last section labelled "PyMOL magic" is NOT curriculum, just a tip!) -->
	:'''Extra material:'''		:'''Extra material:'''
	:*[https://doi.org/10.1093/nar/gkac1077 "RCSB Protein Data Bank (RCSB.org): delivery of experimentally-determined PDB structures alongside one million computed structure models of proteins from artificial intelligence/machine learning"] — article from the annual database issue of Nucleic Acids Research, 2023.		:*[https://doi.org/10.1093/nar/gkac1077 "RCSB Protein Data Bank (RCSB.org): delivery of experimentally-determined PDB structures alongside one million computed structure models of proteins from artificial intelligence/machine learning"] — article from the annual database issue of Nucleic Acids Research, 2023.
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	:'''Slides:''' on DTU Learn.		:'''Slides:''' on DTU Learn.
	:[[Image:Emblem-important_tiny.png‎]] '''Mid-term evaluation:''' Go to https://evaluering.dtu.dk/ and click "Mid-term evaluation" under 22111 [[Image:Emblem-important_tiny.png‎]]		:[[Image:Emblem-important_tiny.png‎]] '''Mid-term evaluation:''' Go to https://evaluering.dtu.dk/ and click "Mid-term evaluation" under 22111 [[Image:Emblem-important_tiny.png‎]]
	:'''Exercise:''' [[Exercise:Malaria Vaccine\|Malaria vaccine]] <!-- — ([[Answers:Malaria Vaccine\|Answers]]) -->		:'''Exercise:''' [[Exercise:Malaria Vaccine\|Malaria vaccine]] <-- — ([[Answers:Malaria Vaccine\|Answers]]) -->

	------		------
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	:'''Slides:''' on DTU Learn.		:'''Slides:''' on DTU Learn.
	:'''Handout''' for the lecture: [[Media:logo_exercise.pdf\|How to construct sequence logos]] (PDF)		:'''Handout''' for the lecture: [[Media:logo_exercise.pdf\|How to construct sequence logos]] (PDF)
	:'''Exercise:''' [[ExSeqLogos\|DNA and Peptide Logos]] <!-- — ([[ExSeqLogosAnswers\|Answers]]) -->		:'''Exercise:''' [[ExSeqLogos\|DNA and Peptide Logos]] <-- — ([[ExSeqLogosAnswers\|Answers]]) -->

	=== Tuesday Oct 31 — Weight matrices and other prediction methods ===		=== Tuesday Oct 31 — Weight matrices and other prediction methods ===
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	<!--:'''Handouts''' for the lecture: -->		<!--:'''Handouts''' for the lecture: -->
	:'''Exercises:'''		:'''Exercises:'''
	:# [[Media:Estimationofpseudocounts_new+examples.pdf\|How to estimate pseudo frequencies]] <!-- ([[Media:Estimationofpseudocounts_answer_brief.pdf\|Answer]]) --> '''Note''': If you solve this manually, just select a couple of amino acids from the table. But if you solve it programmatically (python, Excel, other...), fill out the entire table.		:# [[Media:Estimationofpseudocounts_new+examples.pdf\|How to estimate pseudo frequencies]] <-- ([[Media:Estimationofpseudocounts_answer_brief.pdf\|Answer]]) --> '''Note''': If you solve this manually, just select a couple of amino acids from the table. But if you solve it programmatically (python, Excel, other...), fill out the entire table.
	:# [[Exercise: Construction of sequence logos and weight matrices\|Construction of weight matrices]] <!-- - ([[ExLogo+Matrix-answers\|Answers]]) -->		:# [[Exercise: Construction of sequence logos and weight matrices\|Construction of weight matrices]] <-- - ([[ExLogo+Matrix-answers\|Answers]]) -->
	:'''Link to advanced course: '''		:'''Link to advanced course: '''
	:: [http://teaching.healthtech.dtu.dk/22125/ 22125: Algorithms in bioinformatics]		:: [http://teaching.healthtech.dtu.dk/22125/ 22125: Algorithms in bioinformatics]
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	:'''Curriculum:'''		:'''Curriculum:'''
	:'''Slides:''' on DTU Learn.		:'''Slides:''' on DTU Learn.
	:'''Exercise:''' [[ExPSIBLAST\|PSI-BLAST]] <!-- — ([[ExPSIBLAST_answer\|Answers]]) -->		:'''Exercise:''' [[ExPSIBLAST\|PSI-BLAST]] <-- — ([[ExPSIBLAST_answer\|Answers]]) -->

	=== Tuesday Nov 14 — Multiple alignments ===		=== Tuesday Nov 14 — Multiple alignments ===
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	:'''Curriculum:''' RevTrans ([https://www.ncbi.nlm.nih.gov/pmc/articles/PMC169015/ article])		:'''Curriculum:''' RevTrans ([https://www.ncbi.nlm.nih.gov/pmc/articles/PMC169015/ article])
	:'''Slides:''' on DTU Learn.		:'''Slides:''' on DTU Learn.
	:'''Exercise:''' [[Exercise: Multiple Alignments (Seaview version)\|Multiple Alignments]] <!-- — ([[ExMulAlign-Answers-English\|Answers]]) -->		:'''Exercise:''' [[Exercise: Multiple Alignments (Seaview version)\|Multiple Alignments]] <-- — ([[ExMulAlign-Answers-English\|Answers]]) -->

	=== Tuesday Nov 21 — Phylogenetic trees ===		=== Tuesday Nov 21 — Phylogenetic trees ===
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	:# ''Understanding Evolutionary Trees'', [https://teaching.healthtech.dtu.dk/material/36611/PDF/understanding_evo_trees.pdf PDF].		:# ''Understanding Evolutionary Trees'', [https://teaching.healthtech.dtu.dk/material/36611/PDF/understanding_evo_trees.pdf PDF].
	:'''Slides:''' on DTU Learn.		:'''Slides:''' on DTU Learn.
	:'''Handout''' for lecture: [https://teaching.healthtech.dtu.dk/material/36611/PDF/handout_distance.pdf Reconstructing a distance tree] <!-- ([[Media:handout_distance_answers.pdf\|Answer]]) -->		:'''Handout''' for lecture: [https://teaching.healthtech.dtu.dk/material/36611/PDF/handout_distance.pdf Reconstructing a distance tree] <-- ([[Media:handout_distance_answers.pdf\|Answer]]) -->
	<!-- :'''Software''' for installation: [https://github.com/rambaut/figtree/releases FigTree tree-viewer]		<!-- :'''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.		::'''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.
	:'''TEST''' of the internal webserver we are going to use during the exercise: Please go to https://services.healthtech.dtu.dk/service.php?TreeHugger and click "View <u>example alignment files</u>". Then, copy either the "Sample DNA alignment" or the "Sample peptide dataset" and paste it in the TreeHugger input field. Click <u>Submit query</u> when instructed by the lecturer.		:'''TEST''' of the internal webserver we are going to use during the exercise: Please go to https://services.healthtech.dtu.dk/service.php?TreeHugger and click "View <u>example alignment files</u>". Then, copy either the "Sample DNA alignment" or the "Sample peptide dataset" and paste it in the TreeHugger input field. Click <u>Submit query</u> when instructed by the lecturer.
	-->		-->
	:'''Exercise: [[Exercise: Phylogeny (Seaview version)\|Phylogeny]]''' <!-- — ([[Exercise:_Phylogeny-Answers\|Answers]]) -->		:'''Exercise: [[Exercise: Phylogeny (Seaview version)\|Phylogeny]]''' <-- — ([[Exercise:_Phylogeny-Answers\|Answers]]) -->
	:'''Link to advanced course:'''		:'''Link to advanced course:'''
	::* [http://teaching.healthtech.dtu.dk/22115/ 22115 Computational Molecular Evolution]		::* [http://teaching.healthtech.dtu.dk/22115/ 22115 Computational Molecular Evolution]

WikiSysop at 16:17, 13 March 2024

2024-03-13T16:17:59Z

← Older revision		Revision as of 18:17, 13 March 2024
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	:'''Test of prior knowledge:''' Go to https://evaluering.dtu.dk/, click "Test of prior knowledge" under 22111, and fill out the form (it's anonymous). Spend max. 10 minutes on it.		:'''Test of prior knowledge:''' Go to https://evaluering.dtu.dk/, click "Test of prior knowledge" under 22111, and fill out the form (it's anonymous). Spend max. 10 minutes on it.
	:'''Exercises:'''		:'''Exercises:'''
	:# [[Plain text files and Geany]] <!-- — ([[ExJEdit-Answers\|Answers]]) -->		:# [[Plain text files and Geany]] <-- — ([[ExJEdit-Answers\|Answers]]) -->
	:# [[Taxonomy databases]] <!-- — ([[ExTaxonomy-Answers\|Answers]]) -->		:# [[Taxonomy databases]] <-- — ([[ExTaxonomy-Answers\|Answers]]) -->
	:'''Extra material'''		:'''Extra material'''
	:*"[https://teaching.healthtech.dtu.dk/material/22111/ELS_bioinformatics.pdf Bioinformatics]" — Encyclopedia entry from 2009.		:*"[https://teaching.healthtech.dtu.dk/material/22111/ELS_bioinformatics.pdf Bioinformatics]" — Encyclopedia entry from 2009.

WikiSysop: /* Tuesday Sep 19 — Pairwise alignment */

2024-03-13T16:09:02Z

Tuesday Sep 19 — Pairwise alignment

← Older revision		Revision as of 18:09, 13 March 2024
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	:'''Lecture:''' ''Pairwise alignment'' — Henrik Nielsen.		:'''Lecture:''' ''Pairwise alignment'' — Henrik Nielsen.
	:'''Curriculum:''' Page 35-55 in Immunological Bioinformatics (PDF: on DTU Learn → General information and files → Textbook excerpt).		:'''Curriculum:''' Page 35-55 in Immunological Bioinformatics (PDF: on DTU Learn → General information and files → Textbook excerpt).
	:'''Handout''' for the lecture: [~~[Media~~:New_handout_alignscores.pdf\|Alignment scores]]		:'''Handout''' for the lecture: [https://teaching.healthtech.dtu.dk/material/22111/New_handout_alignscores.pdf Alignment scores]
	:'''Slides:''' on DTU Learn.		:'''Slides:''' on DTU Learn.
	:'''Exercise:''' [[ExPairwiseAlignment\|Pairwise alignment]] <!-- — ([[ExPairwiseAlignment-AnswersEng\|Answers]]) -->		:'''Exercise:''' [[ExPairwiseAlignment\|Pairwise alignment]] <!-- — ([[ExPairwiseAlignment-AnswersEng\|Answers]]) -->