Exercise PSI-BLAST - Revision history

Carol at 16:08, 6 November 2025

2025-11-06T16:08:28Z

← Older revision		Revision as of 18:08, 6 November 2025
Line 134:		Line 134:

	<div style="background-color: lavender; border: solid thin grey;">		<div style="background-color: lavender; border: solid thin grey;">
	:'''Note:''' If BLAST collapses you can check pre-run results using this ID: '''~~GTDKMR8P014~~''' in here [[https://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=GetSaved&RECENT_RESULTS=on Lookup BLAST Job]]		:'''Note:''' If BLAST collapses you can check pre-run results using this ID: '''GTHC3N0F016''' in here [[https://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=GetSaved&RECENT_RESULTS=on Lookup BLAST Job]]
	</div>		</div>

Carol: /* Finding a remote homolog in a specific taxa (Optional) */

2025-11-06T15:45:33Z

Finding a remote homolog in a specific taxa (Optional)

← Older revision		Revision as of 17:45, 6 November 2025
Line 124:		Line 124:
	==Finding a remote homolog in a specific taxa (Optional)==		==Finding a remote homolog in a specific taxa (Optional)==

	PSI-Blast is not only useful for finding a remote homolog in a specific database such as PDB — now it is time to search the broader database "Reference proteins" (<u>refseq_protein</u>). ('''Note:''' we would have liked to do this exercise in the broadest database <u>nr</u>, but that search runs into technical problems). PSI-BLAST can be used in the same way for finding a remote homolog in a specific organism or taxonomic group. Your task in this round is to find out whether the protein with the UniProt ID '''GPAA1_HUMAN''' has a homolog in the genus ''Trypanosoma ~~cruzi~~'' (unicellular parasites which cause diseases like sleeping sickness or Chaga's disease).		PSI-Blast is not only useful for finding a remote homolog in a specific database such as PDB — now it is time to search the broader database "Reference proteins" (<u>refseq_protein</u>). ('''Note:''' we would have liked to do this exercise in the broadest database <u>nr</u>, but that search runs into technical problems). PSI-BLAST can be used in the same way for finding a remote homolog in a specific organism or taxonomic group. Your task in this round is to find out whether the protein with the UniProt ID '''GPAA1_HUMAN''' has a homolog in the genus ''Trypanosoma'' (unicellular parasites which cause diseases like sleeping sickness or Chaga's disease).

	First, try a standard BlastP (where you set <u>Organism</u> to ''Trypanosoma ~~cruzi~~'', <u>Database</u> to <u>refseq_protein</u> ('''not'''		First, try a standard BlastP (where you set <u>Organism</u> to ''Trypanosoma '', <u>Database</u> to <u>refseq_protein</u> ('''not'''
	refseq_select), switch the <u>Low complexity regions</u> filter off, and set the E-value threshold to 10).		refseq_select), switch the <u>Low complexity regions</u> filter off, and set the E-value threshold to 10).
	* '''QUESTION 14''': Do you find any significant (E<0.005) hits? What is the E-value of the best hit?		* '''QUESTION 14''': Do you find any significant (E<0.005) hits? What is the E-value of the best hit?

	Then, try PSI-BLAST. '''Hint:''' You need to search in all organisms (still using refseq_protein) to build a PSSM, then save your PSSM and use that to search in ''Trypanosoma ~~cruzi~~''.		Then, try PSI-BLAST. '''Hint:''' You need to search in all organisms (still using refseq_protein) to build a PSSM, then save your PSSM and use that to search in ''Trypanosoma''.
	* '''QUESTION 15''': How many significant (E<0.005) hits do you find now? What is the E-value of the best hit?		* '''QUESTION 15''': How many significant (E<0.005) hits do you find now? What is the E-value of the best hit?

Carol: /* Finding a remote homolog in a specific taxa (Optional) */

2025-11-06T14:56:30Z

Finding a remote homolog in a specific taxa (Optional)

← Older revision		Revision as of 16:56, 6 November 2025
Line 125:		Line 125:

	PSI-Blast is not only useful for finding a remote homolog in a specific database such as PDB — now it is time to search the broader database "Reference proteins" (<u>refseq_protein</u>). ('''Note:''' we would have liked to do this exercise in the broadest database <u>nr</u>, but that search runs into technical problems). PSI-BLAST can be used in the same way for finding a remote homolog in a specific organism or taxonomic group. Your task in this round is to find out whether the protein with the UniProt ID '''GPAA1_HUMAN''' has a homolog in the genus ''Trypanosoma cruzi'' (unicellular parasites which cause diseases like sleeping sickness or Chaga's disease).		PSI-Blast is not only useful for finding a remote homolog in a specific database such as PDB — now it is time to search the broader database "Reference proteins" (<u>refseq_protein</u>). ('''Note:''' we would have liked to do this exercise in the broadest database <u>nr</u>, but that search runs into technical problems). PSI-BLAST can be used in the same way for finding a remote homolog in a specific organism or taxonomic group. Your task in this round is to find out whether the protein with the UniProt ID '''GPAA1_HUMAN''' has a homolog in the genus ''Trypanosoma cruzi'' (unicellular parasites which cause diseases like sleeping sickness or Chaga's disease).
	* First, try a standard BlastP (where you set <u>Organism</u> to ''Trypanosoma cruzi'', <u>Database</u> to <u>refseq_protein</u> ('''not''' refseq_select), switch the <u>Low complexity regions</u> filter off, and set the E-value threshold to 10).
			First, try a standard BlastP (where you set <u>Organism</u> to ''Trypanosoma cruzi'', <u>Database</u> to <u>refseq_protein</u> ('''not'''
			refseq_select), switch the <u>Low complexity regions</u> filter off, and set the E-value threshold to 10).
	* '''QUESTION 14''': Do you find any significant (E<0.005) hits? What is the E-value of the best hit?		* '''QUESTION 14''': Do you find any significant (E<0.005) hits? What is the E-value of the best hit?
	* Then, try PSI-BLAST. '''Hint:''' You need to search in all organisms (still using refseq_protein) to build a PSSM, then save your PSSM and use that to search in ''Trypanosoma cruzi''.
			Then, try PSI-BLAST. '''Hint:''' You need to search in all organisms (still using refseq_protein) to build a PSSM, then save your PSSM and use that to search in ''Trypanosoma cruzi''.
	* '''QUESTION 15''': How many significant (E<0.005) hits do you find now? What is the E-value of the best hit?		* '''QUESTION 15''': How many significant (E<0.005) hits do you find now? What is the E-value of the best hit?

Carol: /* Finding a remote homolog in a specific taxa (Optional) */

2025-11-06T14:55:55Z

Finding a remote homolog in a specific taxa (Optional)

← Older revision		Revision as of 16:55, 6 November 2025
Line 124:		Line 124:
	==Finding a remote homolog in a specific taxa (Optional)==		==Finding a remote homolog in a specific taxa (Optional)==

	PSI-Blast is not only useful for finding a remote homolog in a specific database such as PDB — now it is time to search the broader database "Reference proteins" (<u>refseq_protein</u>). ('''Note:''' we would have liked to do this exercise in the broadest database <u>nr</u>, but that search runs into technical problems). PSI-BLAST can be used in the same way for finding a remote homolog in a specific organism or taxonomic group. Your task in this round is to find out whether the protein with the UniProt ID '''GPAA1_HUMAN''' has a homolog in the genus ''Trypanosoma'' (unicellular parasites which cause diseases like sleeping sickness or Chaga's disease).		PSI-Blast is not only useful for finding a remote homolog in a specific database such as PDB — now it is time to search the broader database "Reference proteins" (<u>refseq_protein</u>). ('''Note:''' we would have liked to do this exercise in the broadest database <u>nr</u>, but that search runs into technical problems). PSI-BLAST can be used in the same way for finding a remote homolog in a specific organism or taxonomic group. Your task in this round is to find out whether the protein with the UniProt ID '''GPAA1_HUMAN''' has a homolog in the genus ''Trypanosoma cruzi'' (unicellular parasites which cause diseases like sleeping sickness or Chaga's disease).
	* First, try a standard BlastP (where you set <u>Organism</u> to ''Trypanosoma'', <u>Database</u> to <u>refseq_protein</u> ('''not''' refseq_select), switch the <u>Low complexity regions</u> filter off, and set the E-value threshold to 10).		* First, try a standard BlastP (where you set <u>Organism</u> to ''Trypanosoma cruzi'', <u>Database</u> to <u>refseq_protein</u> ('''not''' refseq_select), switch the <u>Low complexity regions</u> filter off, and set the E-value threshold to 10).
	* '''QUESTION 14''': Do you find any significant (E<0.005) hits? What is the E-value of the best hit?		* '''QUESTION 14''': Do you find any significant (E<0.005) hits? What is the E-value of the best hit?
	* Then, try PSI-BLAST. '''Hint:''' You need to search in all organisms (still using refseq_protein) to build a PSSM, then save your PSSM and use that to search in ''Trypanosoma''.		* Then, try PSI-BLAST. '''Hint:''' You need to search in all organisms (still using refseq_protein) to build a PSSM, then save your PSSM and use that to search in ''Trypanosoma cruzi''.
	* '''QUESTION 15''': How many significant (E<0.005) hits do you find now? What is the E-value of the best hit?		* '''QUESTION 15''': How many significant (E<0.005) hits do you find now? What is the E-value of the best hit?

	<div style="background-color: lavender; border: solid thin grey;">		<div style="background-color: lavender; border: solid thin grey;">
	:'''Note:''' If BLAST collapses you can check pre-run results using this ID: '''~~GT51ND2J016~~''' in here [[https://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=GetSaved&RECENT_RESULTS=on Lookup BLAST Job]]		:'''Note:''' If BLAST collapses you can check pre-run results using this ID: '''GTDKMR8P014''' in here [[https://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=GetSaved&RECENT_RESULTS=on Lookup BLAST Job]]
	</div>		</div>

Carol: /* Finding a remote homolog in a specific taxa (Optional) */

2025-11-06T14:52:35Z

Finding a remote homolog in a specific taxa (Optional)

← Older revision		Revision as of 16:52, 6 November 2025
Line 131:		Line 131:

	<div style="background-color: lavender; border: solid thin grey;">		<div style="background-color: lavender; border: solid thin grey;">
	:'''Note:''' If BLAST collapses you can check pre-run results using this ID: '''~~GT3TCGYR016~~''' in here [[https://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=GetSaved&RECENT_RESULTS=on Lookup BLAST Job]]		:'''Note:''' If BLAST collapses you can check pre-run results using this ID: '''GT51ND2J016''' in here [[https://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=GetSaved&RECENT_RESULTS=on Lookup BLAST Job]]
	</div>		</div>

Carol: /* Trying another approach */

2025-11-06T12:34:49Z

Trying another approach

← Older revision		Revision as of 14:34, 6 November 2025
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	* '''QUESTION 2''': How many hits do you obtain (E-value < 10)? ('''Tip:''' you can see the number by selecting all hits (clicking <u>All</u> under <u>Sequences producing significant alignments with E-value BETTER than threshold</u>) and then looking at the number of selected hits)		* '''QUESTION 2''': How many hits do you obtain (E-value < 10)? ('''Tip:''' you can see the number by selecting all hits (clicking <u>All</u> under <u>Sequences producing significant alignments with E-value BETTER than threshold</u>) and then looking at the number of selected hits)

	* '''QUESTION 3''': Excluding the identical match, what is the ~~highest~~ sequence identity ~~(provide sequence Id)~~ and coverage ~~among the hits?~~ Are the hits only human, or do they include other mammals/vertebrates?		* '''QUESTION 3''': Excluding the identical match, what is the match with the lower E-value? Provide sequence Id, %identity and coverage. Are the hits only human, or do they include other mammals/vertebrates?

	* '''QUESTION 4''': Based on the first result, is there a clear homologue in non‐human species? What does that suggest about the gene’s taxonomic distribution?		* '''QUESTION 4''': Based on the first result, is there a clear homologue in non‐human species? What does that suggest about the gene’s taxonomic distribution?

Carol: /* Finding a remote homolog in a specific taxa (Optional) */

2025-11-06T12:08:21Z

Finding a remote homolog in a specific taxa (Optional)

← Older revision		Revision as of 14:08, 6 November 2025
Line 130:		Line 130:
	* '''QUESTION 15''': How many significant (E<0.005) hits do you find now? What is the E-value of the best hit?		* '''QUESTION 15''': How many significant (E<0.005) hits do you find now? What is the E-value of the best hit?

	GT3TCGYR016		<div style="background-color: lavender; border: solid thin grey;">
			:'''Note:''' If BLAST collapses you can check pre-run results using this ID: '''GT3TCGYR016''' in here [[https://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=GetSaved&RECENT_RESULTS=on Lookup BLAST Job]]
			</div>



	<!--		<!--

Carol: /* Finding a remote homolog in a specific taxa (Optional) */

2025-11-06T12:07:01Z

Finding a remote homolog in a specific taxa (Optional)

← Older revision		Revision as of 14:07, 6 November 2025
Line 129:		Line 129:
	* Then, try PSI-BLAST. '''Hint:''' You need to search in all organisms (still using refseq_protein) to build a PSSM, then save your PSSM and use that to search in ''Trypanosoma''.		* Then, try PSI-BLAST. '''Hint:''' You need to search in all organisms (still using refseq_protein) to build a PSSM, then save your PSSM and use that to search in ''Trypanosoma''.
	* '''QUESTION 15''': How many significant (E<0.005) hits do you find now? What is the E-value of the best hit?		* '''QUESTION 15''': How many significant (E<0.005) hits do you find now? What is the E-value of the best hit?

			GT3TCGYR016

	<!--		<!--

Carol: /* Saving and reusing the PSSM */

2025-11-06T11:09:28Z

Saving and reusing the PSSM

← Older revision		Revision as of 13:09, 6 November 2025
Line 111:		Line 111:
	:'''Note:''' If BLAST collapses you can check pre-run results using this ID: '''GT08HV28016''' in here [[https://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=GetSaved&RECENT_RESULTS=on Lookup BLAST Job]]		:'''Note:''' If BLAST collapses you can check pre-run results using this ID: '''GT08HV28016''' in here [[https://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=GetSaved&RECENT_RESULTS=on Lookup BLAST Job]]
	</div>		</div>


	* '''QUESTION 11''': Do you find any significant PDB hits now? Look at the Graphic Summary and query coverage. Is this what you expected, Why?		* '''QUESTION 11''': Do you find any significant PDB hits now? Look at the Graphic Summary and query coverage. Is this what you expected, Why?

Carol: /* Saving and reusing the PSSM */

2025-11-06T11:09:02Z

Saving and reusing the PSSM

← Older revision		Revision as of 13:09, 6 November 2025
Line 109:		Line 109:

	<div style="background-color: lavender; border: solid thin grey;">		<div style="background-color: lavender; border: solid thin grey;">
	:'''Note:''' If BLAST collapses you can check pre-run results using this ID: '''~~GSW70U2V016~~''' in here [[https://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=GetSaved&RECENT_RESULTS=on Lookup BLAST Job]]		:'''Note:''' If BLAST collapses you can check pre-run results using this ID: '''GT08HV28016''' in here [[https://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=GetSaved&RECENT_RESULTS=on Lookup BLAST Job]]
	</div>		</div>