Exercise: BLAST3 - Revision history

Carol: /* BLAST example 2 */

2025-10-01T13:09:41Z

BLAST example 2

← Older revision		Revision as of 15:09, 1 October 2025
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	* '''In conclusion''': What kind of enzyme is CLONE12? Gather as much evidence as possible.		* '''In conclusion''': What kind of enzyme is CLONE12? Gather as much evidence as possible.

	Blast Job ID (blastn): ~~FR5JSVU4016~~		Blast Job ID (blastn): DU9XHV8H014

	Blast Job ID (blastp): ~~FR5MGPK3016~~		Blast Job ID (blastp): DU9T4K44014

Carol: /* Search against Human G+T */

2025-10-01T13:00:44Z

Search against Human G+T

← Older revision		Revision as of 15:00, 1 October 2025
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	Answer the same questions as before about the best hit you found in this search.		Answer the same questions as before about the best hit you found in this search.

	Blast Job ID: ~~FNVWK8TZ016~~		Blast Job ID: DU93YZB1014

	===Concerning database size and E-values===		===Concerning database size and E-values===

Carol: /* Search against NR */

2025-10-01T12:52:27Z

Search against NR

← Older revision		Revision as of 14:52, 1 October 2025
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	:* are there any gaps in the alignment?		:* are there any gaps in the alignment?

	Blast Job ID: ~~FNTVD1B5013~~		Blast Job ID: DU7P2YFF014


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	:Answer the same questions as before about the hit you found now.		:Answer the same questions as before about the hit you found now.

	~~Blast Job ID: FNU1750F013~~

	=== Search against Human G+T ===		=== Search against Human G+T ===

Henni: /* BLAST example 2 */

2024-11-15T15:11:21Z

BLAST example 2

← Older revision		Revision as of 17:11, 15 November 2024
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	* There are two solutions to this:		* There are two solutions to this:
	** Copy the sequence into a text-editor and manually create a FASTA file ("search and replace" and/or "rectangular selection" is useful for the reformatting). <br>This is the most robust solution: it will always work. (Look at the ~~JEdit~~ exercise for a reminder of how to do this).		** Copy the sequence into a text-editor and manually create a FASTA file ("search and replace" and/or "rectangular selection" is useful for the reformatting). <br>This is the most robust solution: it will always work. (Look at [[Plain text files and Geany\|the Geany exercise]] for a reminder of how to do this).
	** Hope the creators of the web-server you're using were kind enough to automatically remove non-DNA letters (paste in ONLY the DNA lines) - this turns out to be the case for both NCBI BLAST and VirtualRibosome, but it ''cannot be universally relied upon''.		** Hope the creators of the web-server you're using were kind enough to automatically remove non-DNA letters (paste in ONLY the DNA lines) - this turns out to be the case for both NCBI BLAST and VirtualRibosome, but it ''cannot be universally relied upon''.

	'''Subquestion''': convert the sequence to FASTA format (manually, in ~~JEdit~~) and quote it in your report.		'''Subquestion''': convert the sequence to FASTA format (manually, in Geany) and quote it in your report.

Carol: /* NCBI */

2024-10-01T06:46:57Z

NCBI

← Older revision		Revision as of 08:46, 1 October 2024
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	Now return to the NCBI blastp page. Set <u>Database</u> to "Reference proteins (refseq_protein)", and enter <tt>Saccharomyces cerevisiae</tt> in the <u>Organism</u> field (and accept the suggestion with taxid:4932).		Now return to the NCBI blastp page. Set <u>Database</u> to "Reference proteins (refseq_protein)", and enter <tt>Saccharomyces cerevisiae</tt> in the <u>Organism</u> field (and accept the suggestion with taxid:4932).

	FR6NDFMJ013		Blast Job ID: FR6NDFMJ013

	[[Image:Office-notes-line_drawing.png\|30px\|left]]		[[Image:Office-notes-line_drawing.png\|30px\|left]]
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	Do as before, still with <u>Database</u> set to "Reference proteins (refseq_protein)", just enter <tt>Human</tt> in the <u>Organism</u> field.		Do as before, still with <u>Database</u> set to "Reference proteins (refseq_protein)", just enter <tt>Human</tt> in the <u>Organism</u> field.

	FR65XVA0016		Blast Job ID: FR65XVA0016

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

Carol: /* Genome specific analysis of histones */

2024-10-01T06:46:26Z

Genome specific analysis of histones

← Older revision		Revision as of 08:46, 1 October 2024
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	Now return to the NCBI blastp page. Set <u>Database</u> to "Reference proteins (refseq_protein)", and enter <tt>Saccharomyces cerevisiae</tt> in the <u>Organism</u> field (and accept the suggestion with taxid:4932).		Now return to the NCBI blastp page. Set <u>Database</u> to "Reference proteins (refseq_protein)", and enter <tt>Saccharomyces cerevisiae</tt> in the <u>Organism</u> field (and accept the suggestion with taxid:4932).

			FR6NDFMJ013

	[[Image:Office-notes-line_drawing.png\|30px\|left]]		[[Image:Office-notes-line_drawing.png\|30px\|left]]
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	Do as before, still with <u>Database</u> set to "Reference proteins (refseq_protein)", just enter <tt>Human</tt> in the <u>Organism</u> field.		Do as before, still with <u>Database</u> set to "Reference proteins (refseq_protein)", just enter <tt>Human</tt> in the <u>Organism</u> field.

			FR65XVA0016

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

Carol: /* Part 3: using BLAST to transfer functional information by finding homologs */

2024-10-01T06:31:57Z

Part 3: using BLAST to transfer functional information by finding homologs

← Older revision		Revision as of 08:31, 1 October 2024
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	* '''In conclusion''': What kind of enzyme is CLONE12? Gather as much evidence as possible.		* '''In conclusion''': What kind of enzyme is CLONE12? Gather as much evidence as possible.

	FR5JSVU4016		Blast Job ID (blastn): FR5JSVU4016

			Blast Job ID (blastp): FR5MGPK3016

Carol: /* BLAST example 2 */

2024-10-01T06:29:29Z

BLAST example 2

← Older revision		Revision as of 08:29, 1 October 2024
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	* You need to copy in small snippets of the BLAST results to document what you observe.		* You need to copy in small snippets of the BLAST results to document what you observe.
	* '''In conclusion''': What kind of enzyme is CLONE12? Gather as much evidence as possible.		* '''In conclusion''': What kind of enzyme is CLONE12? Gather as much evidence as possible.

			FR5JSVU4016

Carol: /* Part 2.0: Create your first Python Notebook */

2024-10-01T03:55:38Z

Part 2.0: Create your first Python Notebook

← Older revision		Revision as of 05:55, 1 October 2024
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	==Part 2.0: Create your first Python Notebook==		==Part 2.0: Create your first Python Notebook==

	[https://colab.research.google.com/drive/~~1Hmv53IiQ5RmuVyGo_DQw9nIpi8vcwxM2~~#scrollTo=~~3gn5prG4QGud~~ Click Here]		[https://colab.research.google.com/drive/1DpqOH8O_KK0rEohjv-20CCx2THwCq89h#scrollTo=_7tJ_S6wc-Os Click Here]

	We are going to make a local copy of this notebook on our own drive.		We are going to make a local copy of this notebook on our own drive.

Carol: /* Random protein sequences and BLASTP */

2024-10-01T03:26:53Z

Random protein sequences and BLASTP

← Older revision		Revision as of 05:26, 1 October 2024
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	[[Image:Office-notes-line_drawing.png\|30px\|left]]		[[Image:Office-notes-line_drawing.png\|30px\|left]]
	:'''QUESTION 2.4''':		:'''QUESTION 2.3''':
	:''(Remember to '''document your answers''' in the same manner as Q2.2)''		:''(Remember to '''document your answers''' in the same manner as Q2.2)''
	<!-- :* How big is the database this time? -->		<!-- :* How big is the database this time? -->
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	[[Image:Office-notes-line_drawing.png\|30px\|left]]		[[Image:Office-notes-line_drawing.png\|30px\|left]]
	:'''QUESTION 2.5''':		:'''QUESTION 2.4''':
	:* If we compare the result from BLAST'ing random DNA sequences to random Peptide sequences - which kind of search has the higher risk of returning false positives (results that appear plausible, maybe even significant, but are truly unrelated)?		:* If we compare the result from BLAST'ing random DNA sequences to random Peptide sequences - which kind of search has the higher risk of returning false positives (results that appear plausible, maybe even significant, but are truly unrelated)?
	:** Remember to take E-values into your consideration.		:** Remember to take E-values into your consideration.