Exercise: The protein database UniProt - Revision history

Henni: /* On your own, with and without AI */

2026-09-07T08:48:11Z

On your own, with and without AI

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	[[Image:Office-notes-line_drawing.png\|30px\|left]] '''QUESTION 4''': Now that you are proficient in UniProt searches, try to answer the following questions. Try each question twice, ''first'' by thinking about the question and using the Advanced Search interface and/or editing the search string, ''second'' by prompting your favorite chatbot (Gemini, ChatGPT, Copilot, Claude, etc.). If the answers differ wildly, try some prompt engineering to make them converge.		[[Image:Office-notes-line_drawing.png\|30px\|left]] '''QUESTION 4''': Now that you are proficient in UniProt searches, try to answer the following questions. Try each question twice, ''first'' by thinking about the question and using the Advanced Search interface and/or editing the search string, ''second'' by prompting your favorite chatbot (Gemini, ChatGPT, Copilot, Claude, etc.). If the answers differ wildly, try some prompt engineering to make them converge.

	Regarding the first approach, remember to write your search string in the answer. Regarding the second approach, write the exact prompts you used.		Regarding the first approach, remember to write your search string in the answer. Regarding the second approach, write the exact prompts you used and state which AI you worked with.
	# Find out how many proteins from ''Escherichia coli'' (all strains) there are in UniProt.		# Find out how many proteins from ''Escherichia coli'' (all strains) there are in UniProt.
	# How many of these are from the notorious pathogenic serotype [https://en.wikipedia.org/wiki/Escherichia_coli_O157:H7 O157:H7] (including its sub-strains)?		# How many of these are from the notorious pathogenic serotype [https://en.wikipedia.org/wiki/Escherichia_coli_O157:H7 O157:H7] (including its sub-strains)?

Henni: /* On your own, with and without AI */

2026-09-06T15:20:55Z

On your own, with and without AI

← Older revision		Revision as of 17:20, 6 September 2026
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	# Find out how many proteins from ''Escherichia coli'' (all strains) there are in UniProt.		# Find out how many proteins from ''Escherichia coli'' (all strains) there are in UniProt.
	# How many of these are from the notorious pathogenic serotype [https://en.wikipedia.org/wiki/Escherichia_coli_O157:H7 O157:H7] (including its sub-strains)?		# How many of these are from the notorious pathogenic serotype [https://en.wikipedia.org/wiki/Escherichia_coli_O157:H7 O157:H7] (including its sub-strains)?
	# Find insulin from as many organisms as possible, without including entries that are not insulin ('''Hint''': If you attempt to do this with the Protein Name field only, it will require an unwieldy amount of kill-words. Therefore, take the gene name into account).		# Find insulin from as many organisms as possible, without including entries that are not insulin ('''Hint''': If you attempt to do this with the Protein Name field only, it will require an unwieldy amount of kill-words. Therefore, take the gene name and/or family into account).
	# Find alpha-globin (the alpha subunit of hemoglobin) from as many ruminants as possible (see the GenBank exercise).		# Find alpha-globin (the alpha subunit of hemoglobin) from as many ruminants as possible (see the GenBank exercise).
	# Find alpha-A globin and alpha-D globin from ''Columba livia'' ('''Hint''': You can use a "*" to perform the search with one search string).		# Find alpha-A globin and alpha-D globin from ''Columba livia'' ('''Hint''': You can use a "*" to perform the search with one search string).

Henni: /* On your own */

2026-09-04T13:32:49Z

On your own

← Older revision		Revision as of 15:32, 4 September 2026
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	:Copy the FASTA sequences to your report.		:Copy the FASTA sequences to your report.

	== On your own ==		== On your own, with and without AI ==

			[[Image:Office-notes-line_drawing.png\|30px\|left]] '''QUESTION 4''': Now that you are proficient in UniProt searches, try to answer the following questions. Try each question twice, ''first'' by thinking about the question and using the Advanced Search interface and/or editing the search string, ''second'' by prompting your favorite chatbot (Gemini, ChatGPT, Copilot, Claude, etc.). If the answers differ wildly, try some prompt engineering to make them converge.

	~~[[Image:Office-notes-line_drawing.png\|30px\|left]] '''QUESTION 4''': Now that you are proficient in UniProt searches, try~~ the ~~following:~~		Regarding the first approach, remember to write your search string in the answer. Regarding the second approach, write the exact prompts you used.

	~~(As always~~, remember to write your search string in the answer).
	# Find out how many proteins from ''Escherichia coli'' (all strains) there are in UniProt.		# Find out how many proteins from ''Escherichia coli'' (all strains) there are in UniProt.
	# How many of these are from the notorious pathogenic serotype [https://en.wikipedia.org/wiki/Escherichia_coli_O157:H7 O157:H7] (including its sub-strains)?		# How many of these are from the notorious pathogenic serotype [https://en.wikipedia.org/wiki/Escherichia_coli_O157:H7 O157:H7] (including its sub-strains)?

Henni: /* Text format */

2026-09-04T10:26:41Z

Text format

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	* '''FT''': Feature Table (annotations pertaining to specified parts of the sequence).		* '''FT''': Feature Table (annotations pertaining to specified parts of the sequence).
	* '''SQ''': Sequence header line.		* '''SQ''': Sequence header line.

			[[Image:Office-notes-line_drawing.png\|30px\|left]]
			:'''QUESTION 2.7:''' Find the two feature table lines that describe the signal peptide and copy them to your answer.

	==Advanced search==		==Advanced search==

Henni: /* Text format */

2026-09-03T16:04:12Z

Text format

← Older revision		Revision as of 18:04, 3 September 2026
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	Until now, we have been working with the graphical user interface to UniProt. However, all the information is also available in plain text format, and that's what you will be working with if you are going to analyze larger amounts of UniProt data later in your studies. For now, let's just have a look at it.		Until now, we have been working with the graphical user interface to UniProt. However, all the information is also available in plain text format, and that's what you will be working with if you are going to analyze larger amounts of UniProt data later in your studies. For now, let's just have a look at it.

	Scroll to the top of the Human Insulin page and find the ~~menu~~ labeled <u>Download</u>. It looks like this: [[File:Download.png]]. Click it, and then ~~''right-~~click'' the ~~option~~ <u>~~Text~~</u> ~~and~~ open it in a new tab. What you see here basically contains all the information you have seen in the graphical interface.		Scroll to the top of the Human Insulin page and find the button labeled <u>Download</u>. <!-- It looks like this: [[File:Download.png]]. -->Click it, and then set <u>Dataset</u> to <u>Entry</u> and <u>Format</u> to <u>Text</u> and click the new <u>Download</u> button. This will open the text format in a new tab. What you see here basically contains all the information you have seen in the graphical interface (except for some information that is retrieved from cross-links, such as the 3D structure).

	Scroll through the plain text file and see if you can find the same information that you just found in the graphical interface. Note that every line starts with a two-letter code specifying the type of the information in the line. Here are some examples:		Scroll through the plain text file and see if you can find the same information that you just found in the graphical interface. Note that every line starts with a two-letter code specifying the type of the information in the line. Here are some examples:

Henni: /* The contents of UniProt */

2026-09-03T15:52:50Z

The contents of UniProt

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	Under the heading <u>Sequence & Isoform</u>, there is a sub-heading named <u>Sequence databases</u>. Here, you can e,g, find links to nucleotide sequences in the databases EMBL / GenBank / DDBJ. Try clicking one of the GenBank links marked "Genomic DNA"; that should take you to a page that looks like something you have seen last week.		Under the heading <u>Sequence & Isoform</u>, there is a sub-heading named <u>Sequence databases</u>. Here, you can e,g, find links to nucleotide sequences in the databases EMBL / GenBank / DDBJ. Try clicking one of the GenBank links marked "Genomic DNA"; that should take you to a page that looks like something you have seen last week.

	Under the heading <u>Structure</u>, there is an interactive window showing a three-dimensional structure of insulin. Note that you can rotate the structure with your mouse. Actually, this structure is not part of UniProt itself, it is a cross-link to the protein structure database PDB. Below the interactive window, you can see the ~~actual~~ cross-links to PDB. Note that PDB is not one single database – just like it was the case for the nucleotide databases, there is a European version (PDBe), an American version (RCSB-PDB), and a Japanese version (PDBj), but luckily, they contain the same data. We will work with the American version of PDB later in the course. As you can see, there are many PDB structures of insulin; in other words, the 3D structure of insulin has been determined several ~~times~~.		[[Image:Office-notes-line_drawing.png\|30px\|left]]
			:'''QUESTION 2.4:'''
			:How many mRNA sequences can you find links to, and what are their identifiers?

			Under the heading <u>Structure</u>, there is an interactive window showing a three-dimensional structure of insulin. Note that you can rotate the structure with your mouse. Actually, this structure is not part of UniProt itself, it is a cross-link to the protein structure database PDB. Below the interactive window, you can see the cross-links to PDB, and you can select which of the cross-linked structures to show by clicking on one of the lines. Note that PDB is not one single database – just like it was the case for the nucleotide databases, there is a European version (PDBe), an American version (RCSB-PDB), and a Japanese version (PDBj), but luckily, they contain the same data. Unlike the nucleotide databases, however, UniProt only provides direct links to one of them, namely PDBe. <!-- We will work with the American version of PDB later in the course. -->As you can see, there are many PDB structures of insulin; in other words, the 3D structure of insulin has been determined many times (under different experimental conditions).

			[[Image:Office-notes-line_drawing.png\|30px\|left]]
			:'''QUESTION 2.5:'''
			:As a default, UniProt displays the first structure in the list. This one shows several copies of the A and B chains. Try clicking the subsequent rows ('''Note:''' don't click the PDB identifier, just click somewhere in the row) until you find a structure that only shows one A chain and one B chain. What is the PDB Identifier of that structure? Insert a screenshot of the 3D structure in your answer.

	Under the heading <u>Family & Domains</u>, there is a subsection named <u>Family and domain databases</u>. It has links to databases containing proteins that are similar (protein families). These have been collected using various techniques that you will hear about later in the course (multiple alignment). In some cases, the proteins are similar only in smaller parts (domains) but not in other parts, and in some cases the databases can tell which parts of the actual protein are known in other species. Some large proteins (not small ones like insulin) can contain several different parts (domains) each with their own evolutionary history. The most important of these databases is InterPro, because it collects the information from most of the other databases. Try to click on one of the InterPro links. This will take you to the Interpro page with lots of information about the protein family that insulin belongs to.		Under the heading <u>Family & Domains</u>, there is a subsection named <u>Family and domain databases</u>. It has links to databases containing proteins that are similar (protein families). These have been collected using various techniques that you will hear about later in the course (multiple alignment). In some cases, the proteins are similar only in smaller parts (domains) but not in other parts, and in some cases the databases can tell which parts of the actual protein are known in other species. Some large proteins (not small ones like insulin) can contain several different parts (domains) each with their own evolutionary history. The most important of these databases is InterPro, because it collects the information from most of the other databases. Try to click on one of the InterPro links. This will take you to the Interpro page with lots of information about the protein family that insulin belongs to.

			[[Image:Office-notes-line_drawing.png\|30px\|left]]
			:'''QUESTION 2.6:'''
			What is the InterPro identifier of the family that is just called "Insulin" and nothing else?

	===Text format===		===Text format===

Henni: /* About strains and subspecies */

2026-09-02T14:43:22Z

About strains and subspecies

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	<!-- Now note the line above the results that says "Expand search "Bacillus subtilis [1423]" to include lower taxonomic ranks" – click it. -->		<!-- Now note the line above the results that says "Expand search "Bacillus subtilis [1423]" to include lower taxonomic ranks" – click it. -->
	The number of ~~entries in Swiss-Prot~~ may seem low for such a well-studied organism. In addition, you may note that there is a link next to the total number of results saying "~~<u>~~or expand search to "1423" to include lower taxonomic ranks</u>". Click it.		The number of hits may seem low for such a well-studied organism. In addition, you may note that there is a link next to the total number of results saying "or expand search to "1423" to <u>include lower taxonomic ranks</u>". Click it.
	<!-- Now do the same thing, but in the field <u>Taxonomy [OC]</u> instead. -->		<!-- Now do the same thing, but in the field <u>Taxonomy [OC]</u> instead. -->

Henni: /* Advanced search */

2026-09-02T14:28:13Z

Advanced search

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	:How many proteins did you find, how many of them are from Swiss-Prot, and what was the search string (the text that appeared in the search field)?		:How many proteins did you find, how many of them are from Swiss-Prot, and what was the search string (the text that appeared in the search field)?

	*''Evidence:'' The proteins we find in this way include proteins that are ''predicted'' to have signal peptides, without necessarily having any experimental evidence for the signal peptides. We will now limit the search to experimentally confirmed signal peptides. Click <u>Advanced</u> again (without erasing your previous search) and change the <u>Evidence</u> menu to <u>~~Any experimental assertion~~</u>.		*''Evidence:'' The proteins we find in this way include proteins that are ''predicted'' to have signal peptides, without necessarily having any experimental evidence for the signal peptides. We will now limit the search to experimentally confirmed signal peptides. Click <u>Advanced</u> again (without erasing your previous search) and change the <u>Evidence</u> menu to <u>Experimental</u>.

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

Henni: /* Simple text mining */

2026-09-02T13:59:53Z

Simple text mining

← Older revision		Revision as of 15:59, 2 September 2026
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	In this case, it was relatively easy to spot the correct hit, but sometimes it is more difficult. If you do not identify the correct hit immediately, it will often help to narrow down the search, and that is exactly what we ask you to do in the next four questions.		In this case, it was relatively easy to spot the correct hit, but sometimes it is more difficult. If you do not identify the correct hit immediately, it will often help to narrow down the search, and that is exactly what we ask you to do in the next four questions.

	The first step is searching for proteins that actually come from the ''organism'' "human" and are ''named'' something containing the word "insulin", as opposed to just ~~containing~~ the words "human" and "insulin" somewhere in the entry.		The first step is searching for proteins that actually come from the ''organism'' "human" and are ''named'' something containing the word "insulin", as opposed to just mentioning the words "human" and "insulin" somewhere in the entry.
	<!-- This can be done very easily: To the left of the results list under <u>Search terms</u> you find a list of links that allow you to restrict the search to specific fields (you may have to scroll down a bit). -->

	On the left, you can see a list of "~~Model~~ organisms". Try to click "Human".		On the left, you can see a list of "Popular organisms". Try to click "Human".
	~~<!-- *Under <u>Filter "human" as:</u> click on: <u>organism</u>. -->~~
	[[Image:Office-notes-line_drawing.png\|30px\|left]]		[[Image:Office-notes-line_drawing.png\|30px\|left]]
	:'''QUESTION 1.2:'''		:'''QUESTION 1.2:'''
	:How many hits are now left? How many of these are from Swiss-Prot?		:How many hits are now left? How many of these are from Swiss-Prot?

	~~<!-- *Under <u>Filter "insulin" as:</u> click on: <u>protein name</u>. -->~~
	However, to really solve the problem, we have to enter Advanced mode. Click on <u>Advanced</u> in the right part of the search field. Search for <tt>human</tt> in the <u>Organism [OS]</u> field, then click <u>Add field</u> and search for <tt>insulin</tt> in the <u>Protein Name [DE]</u> field.		However, to really solve the problem, we have to enter Advanced mode. Click on <u>Advanced</u> in the right part of the search field. Search for <tt>human</tt> in the <u>Organism [OS]</u> field, then click <u>Add field</u> and search for <tt>insulin</tt> in the <u>Protein Name [DE]</u> field.
	[[Image:Office-notes-line_drawing.png\|30px\|left]]		[[Image:Office-notes-line_drawing.png\|30px\|left]]
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	:How many hits are now left? How many of these are from Swiss-Prot? And what has the search string in the text box at the top of the page now turned into?		:How many hits are now left? How many of these are from Swiss-Prot? And what has the search string in the text box at the top of the page now turned into?

	~~<!--~~
	Note that all selections made with the mouse are shown in text format in the search field at the top of the page. It is possible to edit the search criteria manually in this field to make them broader or more narrow.
	*Try for instance to exclude proteins that are not insulin, but only insulin-like. You do this by adding the following text in the search field: '''<tt>NOT name:insulin-like</tt>''' and click on the <u>Search</u> button.
	~~-->~~
	Now, you should exclude proteins that are not insulin, but only insulin-like. Open the <u>Advanced</u> menu again, add a field, make sure it is combined by <u>NOT</u> instead of <u>AND</u>, and remove hits that have <tt>insulin-like</tt> in the protein name.		Now, you should exclude proteins that are not insulin, but only insulin-like. Open the <u>Advanced</u> menu again, add a field, make sure it is combined by <u>NOT</u> instead of <u>AND</u>, and remove hits that have <tt>insulin-like</tt> in the protein name.
	[[Image:Office-notes-line_drawing.png\|30px\|left]]		[[Image:Office-notes-line_drawing.png\|30px\|left]]
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	:How many hits are now left? How many of these are from Swiss-Prot? And what is the search string?		:How many hits are now left? How many of these are from Swiss-Prot? And what is the search string?

	Note that you can also edit the search string directly, instead of going through the ~~Advaced~~ menu every time.		Note that you can also edit the search string directly, instead of going through the Advanced menu every time.
	*Try now to exclude proteins that are insulin receptors (or substrates for insulin receptors).		*Try now to exclude proteins that are insulin receptors (or substrates for insulin receptors).

Henni: /* Simple text mining */

2026-09-02T13:41:25Z

Simple text mining

← Older revision		Revision as of 15:41, 2 September 2026
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	First, we will find some UniProt entries using simple text mining. You are supposed to find the entry for human insulin.		First, we will find some UniProt entries using simple text mining. You are supposed to find the entry for human insulin.

	*Open the UniProt ~~home-page~~ https://www.uniprot.org/		*Open the UniProt homepage https://www.uniprot.org/
	*Type '''<tt>human insulin</tt>''' in the search field in the top of the page. Leave the search menu on "<u>UniProtKB</u>", which is default. Press Enter or click the <u>Search</u> button.		*Type '''<tt>human insulin</tt>''' in the search field in the top of the page. Leave the search menu on "<u>UniProtKB</u>", which is default. Press Enter or click the <u>Search</u> button.
	*If you are new to UniProt, you will be asked whether you want to view your results as "Cards" or "Table". Choose "Table".		*If you are new to UniProt, you will be asked whether you want to view your results as "Cards" or "Table". Choose "Table".