ExSeqLogos v2 - Revision history

Henni: /* Signal peptide comparison */

2026-10-05T11:48:15Z

Signal peptide comparison

Raz: /* Part 0: Getting to know "LogoLab" */

2026-10-01T19:51:50Z

Part 0: Getting to know "LogoLab"

← Older revision		Revision as of 21:51, 1 October 2026
Line 37:		Line 37:
	With the DNA example do the following:		With the DNA example do the following:
	# Play around with the '''logo model''' - make sure you understand what each model is about (cross-ref with the lecture slides).		# Play around with the '''logo model''' - make sure you understand what each model is about (cross-ref with the lecture slides).
	# Return to "Shannon information" as the model, and ~~observer~~ what happens in the "Inspector" view (scroll down a little bit to see it) when you click a position in the LOGO.		# Return to "Shannon information" as the model, and observe what happens in the "Inspector" view (scroll down a little bit to see it) when you click a position in the LOGO.
	# Make sure you understand why the 1st position has an information content of 2.0 bits, and the 3rd position has an information content of 1.0 bits. Make sure you understand the scaling (heights) of the letters - think about it in the context of the hand-out exercise we did together during the lecture.		# Make sure you understand why the 1st position has an information content of 2.0 bits, and the 3rd position has an information content of 1.0 bits. Make sure you understand the scaling (heights) of the letters - think about it in the context of the hand-out exercise we did together during the lecture.
	# Add error-bars to your plot and, play around with the "Display option" to do on-the-fly rescaling of the LOGO plot, and test the option for downloading the plot to you own computer (PNG is likely the easiest to use). Notice that '''you can set a title for your plot''' using the display options.		# Add error-bars to your plot and, play around with the "Display option" to do on-the-fly rescaling of the LOGO plot, and test the option for downloading the plot to you own computer (PNG is likely the easiest to use). Notice that '''you can set a title for your plot''' using the display options.

Henni: /* Introducing Seq2Logo */

2026-10-01T18:44:04Z

Introducing Seq2Logo

← Older revision		Revision as of 20:44, 1 October 2026
Line 238:		Line 238:
	</div>		</div>

	As the next step we shall investigate how to work with the '''Seq2Logo''' tool hosted locally here at DTU. It offers a lot more advanced functionality with regards to the algorithms behind the plots, and many of these functions we'll get back to ~~next week~~ when we work with '''weight matrices'''.		As the next step we shall investigate how to work with the '''Seq2Logo''' tool hosted locally here at DTU. It offers a lot more advanced functionality with regards to the algorithms behind the plots, and many of these functions we'll get back to later in the course when we work with '''weight matrices'''.

	'''TASK:''' create a basic LOGO plot for the '''eukaryote''' dataset		'''TASK:''' create a basic LOGO plot for the '''eukaryote''' dataset

Henni: /* Introducing Seq2Logo */

2026-10-01T18:19:12Z

Introducing Seq2Logo

← Older revision		Revision as of 20:19, 1 October 2026
Line 235:		Line 235:
	=== Introducing Seq2Logo ===		=== Introducing Seq2Logo ===
	<div style="background-color: lavender; border: solid thin grey;">		<div style="background-color: lavender; border: solid thin grey;">
	'''2026 note:''' The new LogoLab webapp also provides the needed functionality for this part, but it's a little less tested on KL logos. Once you have done the part below with seq2logo (which we'll also be using ~~next week~~) you're welcome to try to solve the same questions using LogoLab and give us feedback. Thanks.		'''2026 note:''' The new LogoLab webapp also provides the needed functionality for this part, but it's a little less tested on KL logos. Once you have done the part below with seq2logo (which we'll also be using while working with weight matrices) you're welcome to try to solve the same questions using LogoLab and give us feedback. Thanks.
	</div>		</div>

Henni: /* Investigating the peptide example */

2026-10-01T18:12:43Z

Investigating the peptide example

← Older revision		Revision as of 20:12, 1 October 2026
Line 47:		Line 47:
	# As we talked about in class, background correction is much more important for protein sequences. Try out the different logo models, and notice that the KL model can make a substantial difference.		# As we talked about in class, background correction is much more important for protein sequences. Try out the different logo models, and notice that the KL model can make a substantial difference.
	# With the KL model active, click though some of the positions where many AA's are seen in the data, and look at the data in the Inspector view. Make sure you understand where p and q comes from, and how they affect the calculations.		# With the KL model active, click though some of the positions where many AA's are seen in the data, and look at the data in the Inspector view. Make sure you understand where p and q comes from, and how they affect the calculations.
	# Pseudo-counts: we'll learn much more about them ~~next week~~, but they are essentially a way have a best guess of amino-acid ~~frequecies~~ we might see if we had a larger data set (including the amino-acids we have not seen in out data). Try to briefly click them on ~~anf~~ off to see (visually) what that do - I'll return to them ~~next week~~.		# Pseudo-counts: we'll learn much more about them later in the course, but they are essentially a way to have a best guess of amino-acid frequencies we might see if we had a larger data set (including the amino-acids we have not seen in out data). Try to briefly click them on and off to see (visually) what that do - I'll return to them later in the course.

	= Part 1: DNA logos (scientific case) =		= Part 1: DNA logos (scientific case) =

Henni: /* Investigating the DNA example */

2026-10-01T18:10:29Z

Investigating the DNA example

← Older revision		Revision as of 20:10, 1 October 2026
Line 39:		Line 39:
	# Return to "Shannon information" as the model, and observer what happens in the "Inspector" view (scroll down a little bit to see it) when you click a position in the LOGO.		# Return to "Shannon information" as the model, and observer what happens in the "Inspector" view (scroll down a little bit to see it) when you click a position in the LOGO.
	# Make sure you understand why the 1st position has an information content of 2.0 bits, and the 3rd position has an information content of 1.0 bits. Make sure you understand the scaling (heights) of the letters - think about it in the context of the hand-out exercise we did together during the lecture.		# Make sure you understand why the 1st position has an information content of 2.0 bits, and the 3rd position has an information content of 1.0 bits. Make sure you understand the scaling (heights) of the letters - think about it in the context of the hand-out exercise we did together during the lecture.
	# Add error-bars to your plot and, play around with the "Display option" to do on-the-fly rescaling of the LOGO plot, and test the option for downloading the plot to you own computer (PNG is likely the easiest to use). Notice that '''you can set a title for ~~you~~ plot''' using the display options.		# Add error-bars to your plot and, play around with the "Display option" to do on-the-fly rescaling of the LOGO plot, and test the option for downloading the plot to you own computer (PNG is likely the easiest to use). Notice that '''you can set a title for your plot''' using the display options.

	== Investigating the peptide example ==		== Investigating the peptide example ==

Henni: /* LogoLab (DTU) */

2026-10-01T18:03:31Z

LogoLab (DTU)

← Older revision		Revision as of 20:03, 1 October 2026
Line 5:		Line 5:
	== LogoLab (DTU) ==		== LogoLab (DTU) ==
	[[image:LogoLab_Sep2026.png\|500px\|right]]		[[image:LogoLab_Sep2026.png\|500px\|right]]
	For this exercise we'll use a tool specifically ~~build~~ for experimentation with LOGO plots and for building understanding of how they work internally.		For this exercise we'll use a tool specifically built for experimentation with LOGO plots and for building understanding of how they work internally.

	'''Link:''' https://wernersson.dk/logolab/ (~~Build~~ by Rasmus Wernersson, it'll migrate to a DTU server soon).		'''Link:''' https://wernersson.dk/logolab/ (Built by Rasmus Wernersson, it'll migrate to a DTU server soon).

	'''Points of notice:'''		'''Points of notice:'''
	* It runs entirely in your browser, and allows for very quick ~~experimentarion~~ with the visualization.		* It runs entirely in your browser, and allows for very quick experimentation with the visualization.
	* ~~The~~ is a stand-alone downloadable build available for running locally on ~~you~~ own machine.		* There is a stand-alone downloadable build available for running locally on your own machine.
	* It comes with an "Inspector" functionality that allows you to "~~peak~~ inside" each position in the LOGO to see the numbers behind the visuals.		* It comes with an "Inspector" functionality that allows you to "peek inside" each position in the LOGO to see the numbers behind the visuals.
	* It has an extensive help-page going over all the equations used.		* It has an extensive help-page going over all the equations used.

Raz: /* Seq2Logo (CBS/DTU) */

2026-10-01T06:24:10Z

Seq2Logo (CBS/DTU)

← Older revision		Revision as of 08:24, 1 October 2026
Line 23:		Line 23:

	A more advanced method for working with '''peptide''' sequences.		A more advanced method for working with '''peptide''' sequences.

			We'll introduce it briefly here, and get back to it in more details when we get to work with weight matrices.
	<br style="clear: both" />		<br style="clear: both" />

Raz: /* Seq2Logo (CBS/DTU) */

2026-10-01T06:22:53Z

Seq2Logo (CBS/DTU)

← Older revision		Revision as of 08:22, 1 October 2026
Line 23:		Line 23:

	A more advanced method for working with '''peptide''' sequences.		A more advanced method for working with '''peptide''' sequences.
			<br style="clear: both" />

	= Part 0: Getting to know "LogoLab" =		= Part 0: Getting to know "LogoLab" =

Raz: /* LogoLab (DTU) */

2026-10-01T06:22:44Z

LogoLab (DTU)

← Older revision		Revision as of 08:22, 1 October 2026
Line 4:		Line 4:

	== LogoLab (DTU) ==		== LogoLab (DTU) ==
			[[image:LogoLab_Sep2026.png\|500px\|right]]
	For this exercise we'll use a tool specifically build for experimentation with LOGO plots and for building understanding of how they work internally.		For this exercise we'll use a tool specifically build for experimentation with LOGO plots and for building understanding of how they work internally.

Line 15:		Line 16:

	It you want a good command-line tool as well, we'll recommend the "weblogo" program (Berkeley, not DTU) - it can be downloaded here: http://weblogo.berkeley.edu/		It you want a good command-line tool as well, we'll recommend the "weblogo" program (Berkeley, not DTU) - it can be downloaded here: http://weblogo.berkeley.edu/
			<br style="clear: both" />

	== Seq2Logo (CBS/DTU) ==		== Seq2Logo (CBS/DTU) ==

← Older revision		Revision as of 13:48, 5 October 2026
Line 218:		Line 218:
	=== Signal peptide comparison ===		=== Signal peptide comparison ===
	'''OVERALL TASK:'''		'''OVERALL TASK:'''
	* Generating peptide LOGOs with the ~~WebLogo~~ resource is as straightforward as before, and your goal is to '''compare''' the motifs in the signal peptides across the three taxonomical groups.		* Generating peptide LOGOs with the Logo Lab resource is as straightforward as before, and your goal is to '''compare''' the motifs in the signal peptides across the three taxonomical groups.
	* Play around with the options (dimensions~~, Y-axis scaling, tics~~ etc) as much as you like, but '''make sure that''':		* Play around with the options (dimensions etc) as much as you like, but '''make sure that''':
	*# It's easy to compare the plots (put in ~~labels~~ etc)		*# It's easy to compare the plots (put in titles etc)
	*# The y-axis scaling must be the same across the 3 plots		<!-- *# The y-axis scaling must be the same across the 3 plots -->
	*# Plot the '''signal peptide part''' of the sequences in '''negative numbers'''		*# Plot the '''signal peptide part''' of the sequences in '''negative numbers'''
	*# Read up on what the coloring means (~~click~~ the ~~"?" in "color scheme~~) - this will help you interpret the results.		*# Read up on what the "Chemistry" coloring means (see below the plot) - this will help you interpret the results.

	[[Image:Office-notes-line_drawing.png\|30px\|left]]		[[Image:Office-notes-line_drawing.png\|30px\|left]]
Line 233:		Line 233:

	-------		-------

	=== Introducing Seq2Logo ===		=== Introducing Seq2Logo ===
	<div style="background-color: lavender; border: solid thin grey;">		<div style="background-color: lavender; border: solid thin grey;">