Exercise: Multiple Alignments (English version) - Revision history

WikiSysop: /* Step 3 */

2024-03-13T15:04:54Z

Step 3

← Older revision		Revision as of 17:04, 13 March 2024
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	===Step 3===		===Step 3===
	Now translate the DNA sequences to protein sequences and construct a new alignment.		Now translate the DNA sequences to protein sequences and construct a new alignment.
	Link: [https://services.healthtech.dtu.dk/~~service~~.~~php?VirtualRibosome VirtualRibosome]~~		Link: https://services.healthtech.dtu.dk/services/VirtualRibosome-2.0/

	[[Image:Office-notes-line_drawing.png\|30px\|left]]		[[Image:Office-notes-line_drawing.png\|30px\|left]]

WikiSysop: /* Step 8 */

2024-03-13T15:04:18Z

Step 8

← Older revision		Revision as of 17:04, 13 March 2024
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	The data set for this part of the exercise will be a cleaned-up version of the Insulin FASTA file from Step 4 above (redundancy reduced and with short informative names), available via [https://teaching.healthtech.dtu.dk/material/22111/Insulin_processed.fasta this link].		The data set for this part of the exercise will be a cleaned-up version of the Insulin FASTA file from Step 4 above (redundancy reduced and with short informative names), available via [https://teaching.healthtech.dtu.dk/material/22111/Insulin_processed.fasta this link].

	Link to the RevTrans 2.0 server: https://services.healthtech.dtu.dk/~~service~~.~~php?RevTrans~~		Link to the RevTrans 2.0 server: https://services.healthtech.dtu.dk/services/RevTrans-2.0/

	Notice that it's possible to specify which translation table to use. You may recognize the options from ''VirtualRibosome''. This is no coincidence: both servers are using the same underlying algorithm for translating DNA to protein.		Notice that it's possible to specify which translation table to use. You may recognize the options from ''VirtualRibosome''. This is no coincidence: both servers are using the same underlying algorithm for translating DNA to protein.

WikiSysop: /* Step 8 */

2024-03-13T15:03:32Z

Step 8

← Older revision		Revision as of 17:03, 13 March 2024
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	'''If you haven't read [https://www.ncbi.nlm.nih.gov/pmc/articles/PMC169015/ the RevTrans paper] yet — please quickly skim through it now''' (it's an easy read). The paper explains the concept behind the RevTrans method in details (DNA → Protein; Multiple alignment of the proteins; Construct DNA alignment from the DNA sequences using the peptide alignment as a scaffold).		'''If you haven't read [https://www.ncbi.nlm.nih.gov/pmc/articles/PMC169015/ the RevTrans paper] yet — please quickly skim through it now''' (it's an easy read). The paper explains the concept behind the RevTrans method in details (DNA → Protein; Multiple alignment of the proteins; Construct DNA alignment from the DNA sequences using the peptide alignment as a scaffold).

	The data set for this part of the exercise will be a cleaned-up version of the Insulin FASTA file from Step 4 above (redundancy reduced and with short informative names), available via [~~[Media~~:~~insulin_processed~~.fasta\|this link]].		The data set for this part of the exercise will be a cleaned-up version of the Insulin FASTA file from Step 4 above (redundancy reduced and with short informative names), available via [https://teaching.healthtech.dtu.dk/material/22111/Insulin_processed.fasta this link].

	Link to the RevTrans 2.0 server: https://services.healthtech.dtu.dk/service.php?RevTrans		Link to the RevTrans 2.0 server: https://services.healthtech.dtu.dk/service.php?RevTrans

WikiSysop: /* Intermezzo - alternative splicing & protein isoforms */

2024-03-13T14:59:16Z

Intermezzo - alternative splicing & protein isoforms

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	==Intermezzo - alternative splicing & protein isoforms ==		==Intermezzo - alternative splicing & protein isoforms ==
	[[Image:SpliceForms_raz_cropped.png\|thumb\|right\|600px\|Overview of different types of alternative splicing.]] '''[https://teaching.healthtech.dtu.dk/material/22111/SpliceForms_raz_cropped.pdf CLICK HERE to view full screen PDF version]'''.		[[Image:SpliceForms_raz_cropped.png\|thumb\|right\|600px\|Overview of different types of alternative splicing. '''[https://teaching.healthtech.dtu.dk/material/22111/SpliceForms_raz_cropped.pdf CLICK HERE to view full screen PDF version]''']] .
	In the alignments we have been working with so far, the proteins have been related by evolution; either orthologous proteins from different organisms or paralogous proteins from the same organism (e.g. alpha-A and alpha-D globin). Now, we will work with a dataset of proteins related by ''alternative splicing'': In some genes, introns can be spliced out of the transcript in more than one way, with the consequence that the same gene can produce a number of different proteins (isoforms). There are several kinds of alternative splicing, summarized in the figure to the right.		In the alignments we have been working with so far, the proteins have been related by evolution; either orthologous proteins from different organisms or paralogous proteins from the same organism (e.g. alpha-A and alpha-D globin). Now, we will work with a dataset of proteins related by ''alternative splicing'': In some genes, introns can be spliced out of the transcript in more than one way, with the consequence that the same gene can produce a number of different proteins (isoforms). There are several kinds of alternative splicing, summarized in the figure to the right.

WikiSysop: /* Intermezzo - alternative splicing & protein isoforms */

2024-03-13T14:58:18Z

Intermezzo - alternative splicing & protein isoforms

← Older revision		Revision as of 16:58, 13 March 2024
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	==Intermezzo - alternative splicing & protein isoforms ==		==Intermezzo - alternative splicing & protein isoforms ==
	[[Image:SpliceForms_raz_cropped.png\|thumb\|right\|600px\|Overview of different types of alternative splicing. '''[[https://teaching.healthtech.dtu.dk/material/22111/SpliceForms_raz_cropped.pdf CLICK HERE to view full screen PDF version]]'''.]		[[Image:SpliceForms_raz_cropped.png\|thumb\|right\|600px\|Overview of different types of alternative splicing.]] '''[https://teaching.healthtech.dtu.dk/material/22111/SpliceForms_raz_cropped.pdf CLICK HERE to view full screen PDF version]'''.
	In the alignments we have been working with so far, the proteins have been related by evolution; either orthologous proteins from different organisms or paralogous proteins from the same organism (e.g. alpha-A and alpha-D globin). Now, we will work with a dataset of proteins related by ''alternative splicing'': In some genes, introns can be spliced out of the transcript in more than one way, with the consequence that the same gene can produce a number of different proteins (isoforms). There are several kinds of alternative splicing, summarized in the figure to the right.		In the alignments we have been working with so far, the proteins have been related by evolution; either orthologous proteins from different organisms or paralogous proteins from the same organism (e.g. alpha-A and alpha-D globin). Now, we will work with a dataset of proteins related by ''alternative splicing'': In some genes, introns can be spliced out of the transcript in more than one way, with the consequence that the same gene can produce a number of different proteins (isoforms). There are several kinds of alternative splicing, summarized in the figure to the right.

WikiSysop: /* Intermezzo - alternative splicing & protein isoforms */

2024-03-13T14:56:58Z

Intermezzo - alternative splicing & protein isoforms

← Older revision		Revision as of 16:56, 13 March 2024
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	==Intermezzo - alternative splicing & protein isoforms ==		==Intermezzo - alternative splicing & protein isoforms ==
	[[Image:SpliceForms_raz_cropped.png\|thumb\|right\|600px\|Overview of different types of alternative splicing. '''[https://teaching.healthtech.dtu.dk/material/22111/SpliceForms_raz_cropped.pdf CLICK HERE to view full screen PDF version]'''.]		[[Image:SpliceForms_raz_cropped.png\|thumb\|right\|600px\|Overview of different types of alternative splicing. '''[[https://teaching.healthtech.dtu.dk/material/22111/SpliceForms_raz_cropped.pdf CLICK HERE to view full screen PDF version]]'''.]
	In the alignments we have been working with so far, the proteins have been related by evolution; either orthologous proteins from different organisms or paralogous proteins from the same organism (e.g. alpha-A and alpha-D globin). Now, we will work with a dataset of proteins related by ''alternative splicing'': In some genes, introns can be spliced out of the transcript in more than one way, with the consequence that the same gene can produce a number of different proteins (isoforms). There are several kinds of alternative splicing, summarized in the figure to the right.		In the alignments we have been working with so far, the proteins have been related by evolution; either orthologous proteins from different organisms or paralogous proteins from the same organism (e.g. alpha-A and alpha-D globin). Now, we will work with a dataset of proteins related by ''alternative splicing'': In some genes, introns can be spliced out of the transcript in more than one way, with the consequence that the same gene can produce a number of different proteins (isoforms). There are several kinds of alternative splicing, summarized in the figure to the right.

WikiSysop: /* Intermezzo - alternative splicing & protein isoforms */

2024-03-13T14:56:10Z

Intermezzo - alternative splicing & protein isoforms

← Older revision		Revision as of 16:56, 13 March 2024
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	==Intermezzo - alternative splicing & protein isoforms ==		==Intermezzo - alternative splicing & protein isoforms ==
	[[Image:SpliceForms_raz_cropped.png\|thumb\|right\|600px\|Overview of different types of alternative splicing. '''[~~[Media~~:SpliceForms_raz_cropped.pdf\|CLICK HERE to view full screen PDF version]]'''.]]		[[Image:SpliceForms_raz_cropped.png\|thumb\|right\|600px\|Overview of different types of alternative splicing. '''[https://teaching.healthtech.dtu.dk/material/22111/SpliceForms_raz_cropped.pdf CLICK HERE to view full screen PDF version]'''.]
	In the alignments we have been working with so far, the proteins have been related by evolution; either orthologous proteins from different organisms or paralogous proteins from the same organism (e.g. alpha-A and alpha-D globin). Now, we will work with a dataset of proteins related by ''alternative splicing'': In some genes, introns can be spliced out of the transcript in more than one way, with the consequence that the same gene can produce a number of different proteins (isoforms). There are several kinds of alternative splicing, summarized in the figure to the right.		In the alignments we have been working with so far, the proteins have been related by evolution; either orthologous proteins from different organisms or paralogous proteins from the same organism (e.g. alpha-A and alpha-D globin). Now, we will work with a dataset of proteins related by ''alternative splicing'': In some genes, introns can be spliced out of the transcript in more than one way, with the consequence that the same gene can produce a number of different proteins (isoforms). There are several kinds of alternative splicing, summarized in the figure to the right.

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	We are now going to investigate how three different alignment programs perform on a dataset of isoforms from one particular gene.		We are now going to investigate how three different alignment programs perform on a dataset of isoforms from one particular gene.

	[~~[Media~~:EPB4.1_human.fasta\|Here]] is a dataset consisting of 11 alternatively-spliced gene products from the human erythrocyte membrane protein band 4.1 (EPB). The goal of this exercise is to compare how well three different popular multiple alignment programs perform when attempting to align a set of proteins that are identical except for having different deletions.		[https://teaching.healthtech.dtu.dk/material/22111/EPB4.1_human.fasta Here is a dataset] consisting of 11 alternatively-spliced gene products from the human erythrocyte membrane protein band 4.1 (EPB). The goal of this exercise is to compare how well three different popular multiple alignment programs perform when attempting to align a set of proteins that are identical except for having different deletions.

	Align the EPB sequences using the MAFFT, MUSCLE, and Kalign servers at [http://www.ebi.ac.uk/Tools/msa/ the EBI Multiple Sequence Alignment page] with Clustalw as output format. For each alignment, keep the window (or tab) open after use.		Align the EPB sequences using the MAFFT, MUSCLE, and Kalign servers at [http://www.ebi.ac.uk/Tools/msa/ the EBI Multiple Sequence Alignment page] with Clustalw as output format. For each alignment, keep the window (or tab) open after use.

WikiSysop: /* Step 4 */

2024-03-13T14:50:47Z

Step 4

← Older revision		Revision as of 16:50, 13 March 2024
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	===Step 4===		===Step 4===
	'''New data set: Insulin'''. [~~[Media~~:~~insulin_raw~~.fasta\|This FASTA file]] contains the DNA sequence from the Insulin gene from a range of organisms		'''New data set: Insulin'''. [https://teaching.healthtech.dtu.dk/material/22111/Insulin_raw.fasta This FASTA file] contains the DNA sequence from the Insulin gene from a range of organisms

	Notice that this FASTA file has been auto-generated from a database, and it is currently not that informative with regards to entry names. Before we carry on with the analysis, you need to figure out '''which organisms''' the sequences belong to by '''looking up the entries in GenBank'''. Based on this information construct a '''new FASTA file''' with names that 1) describe what organism each sequence came from and 2) keep in the GenBank ID for later reference.		Notice that this FASTA file has been auto-generated from a database, and it is currently not that informative with regards to entry names. Before we carry on with the analysis, you need to figure out '''which organisms''' the sequences belong to by '''looking up the entries in GenBank'''. Based on this information construct a '''new FASTA file''' with names that 1) describe what organism each sequence came from and 2) keep in the GenBank ID for later reference.

WikiSysop: /* Step 1 */

2024-03-13T14:47:26Z

Step 1

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	Copy each DNA sequence into your text editor as you find it. Give it a descriptive name that conveys which '''organism''' it comes from, and what '''type of alpha-globin''' it is. '''Remember to save your work often'''.		Copy each DNA sequence into your text editor as you find it. Give it a descriptive name that conveys which '''organism''' it comes from, and what '''type of alpha-globin''' it is. '''Remember to save your work often'''.

	'''Important:''' Always use the gene/protein name ''from the CDS feature'', not the GenBank entry name. (There is a trap buried somewhere here, where the entry name is directly misleading). See this PDF: [https://teaching.healthtech.dtu.dk/material/MultiGeneScreenshot-en.pdf How to locate CDS names in GenBank].		'''Important:''' Always use the gene/protein name ''from the CDS feature'', not the GenBank entry name. (There is a trap buried somewhere here, where the entry name is directly misleading). See this PDF: [https://teaching.healthtech.dtu.dk/material/22111/MultiGeneScreenshot-en.pdf How to locate CDS names in GenBank].

	[[Image:Office-notes-line_drawing.png\|30px\|left]]		[[Image:Office-notes-line_drawing.png\|30px\|left]]

WikiSysop: /* Step 1 */

2024-03-13T14:47:01Z

Step 1

← Older revision		Revision as of 16:47, 13 March 2024
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	Copy each DNA sequence into your text editor as you find it. Give it a descriptive name that conveys which '''organism''' it comes from, and what '''type of alpha-globin''' it is. '''Remember to save your work often'''.		Copy each DNA sequence into your text editor as you find it. Give it a descriptive name that conveys which '''organism''' it comes from, and what '''type of alpha-globin''' it is. '''Remember to save your work often'''.

	'''Important:''' Always use the gene/protein name ''from the CDS feature'', not the GenBank entry name. (There is a trap buried somewhere here, where the entry name is directly misleading). See this PDF: [~~[Media~~:MultiGeneScreenshot-en.pdf\|How to locate CDS names in GenBank]].		'''Important:''' Always use the gene/protein name ''from the CDS feature'', not the GenBank entry name. (There is a trap buried somewhere here, where the entry name is directly misleading). See this PDF: [https://teaching.healthtech.dtu.dk/material/MultiGeneScreenshot-en.pdf How to locate CDS names in GenBank].

	[[Image:Office-notes-line_drawing.png\|30px\|left]]		[[Image:Office-notes-line_drawing.png\|30px\|left]]