Exercise:BLAST new - Revision history

Carol: /* Random protein sequences and BLASTP */

2026-09-22T08:57:59Z

Random protein sequences and BLASTP

← Older revision		Revision as of 09:57, 22 September 2026
Line 268:		Line 268:
	Now it's time to work with a set of '''protein sequences''': Generate 10 peptide sequences of length 25aa using Google colab.		Now it's time to work with a set of '''protein sequences''': Generate 10 peptide sequences of length 25aa using Google colab.

	~~:'''Notice 1:''' The distribution of amino acids~~ will ~~be equal (5% prob) and this is different from true biological sequences - however this is not important for this first part of the exercise.~~		In our Google colab we will now select <u>blastp</u> as the algorithm to use, and the "NR" database (this is the protein version, consisting of translated CDS'es, UniProt etc).
	~~:'''Notice 2:''' Please recall from the lecture that the way~~ <tt>~~BLASTP~~</tt> ~~selects candidate sequences for full Smith-Waterman alignment is different from <tt>BLASTN</tt>.~~ (~~<tt>BLASTN</tt> - a single short (11 bp +) perfect match hit~~ is ~~needed. <tt>BLASTP</tt> - a pair~~ of ~~"near match" hits of 3 aa within a 40 aa window is needed~~).

			:'''Note 1:''' In our random generated sequences, the distribution of amino acids will be equal (5% prob) and this is different from true biological sequences - however this is not important for this first part of the exercise.
			:'''Note 2:''' Please recall from the lecture that the way <tt>BLASTP</tt> selects candidate sequences for full Smith-Waterman alignment is different from <tt>BLASTN</tt>. (<tt>BLASTN</tt> - a single short (11 bp +) perfect match hit is needed. <tt>BLASTP</tt> - a pair of "near match" hits of 3 aa within a 40 aa window is needed). We also need to tweak the parameters this time. We are doing this by "<u>short_query =False</u>", which will be analogous to set in the Web browser version "<u>Algorithm Parameters</u>" section select BLOSUM62 as the alignment matrix to use and set the "<u>Expect threshold</u>" to 1000 (default: 10).

	~~Choose <u>blastp</u> as the algorithm to use, the "NR" database (this is the protein version, consisting of translated CDS'es, UniProt etc).~~

	'''VERY IMPORTANT''': We also need to tweak the parameters this time - in the "<u>Algorithm Parameters</u>" section select BLOSUM62 as the alignment matrix to use and set the "<u>Expect threshold</u>" to 1000 (default: 10).

	Perform the BLAST search.		Perform the BLAST search.
	Inspect the results.		Inspect the results.


	[[Image:Office-notes-line_drawing.png\|30px\|left]]		[[Image:Office-notes-line_drawing.png\|30px\|left]]
	:'''QUESTION 2.3''':		:'''QUESTION 2.3''':
	:''(~~Remember to~~ '''document your answers''' in the same manner as Q2.1)''		:''(Please '''document your answers''' in the same manner as Q2.1)''
	<!-- :* How big is the database this time? -->		<!-- :* How big is the database this time? -->
	:* What is the typical length of the alignment and do they contain gaps?		:* What is the typical length of the alignment and do they contain gaps?

Carol: /* Random DNA sequences and BLASTN */

2026-09-22T08:36:24Z

Random DNA sequences and BLASTN

← Older revision		Revision as of 09:36, 22 September 2026
Line 241:		Line 241:
	In Google Colab, this will be analogous to the web browser using the option "blastn" in the section "<u>Program Selection</u>". And in this case we will select "<u>Nucleotide Collection (nr/nt)</u>" as the search database. In addition we will have to modify the E-value cut-off ("<u>E_VALUE_THRESH</u>") to '''50'''		In Google Colab, this will be analogous to the web browser using the option "blastn" in the section "<u>Program Selection</u>". And in this case we will select "<u>Nucleotide Collection (nr/nt)</u>" as the search database. In addition we will have to modify the E-value cut-off ("<u>E_VALUE_THRESH</u>") to '''50'''

	'''~~VERY IMPORTANT~~''':		'''Note''': For this special situation where we BLAST small artificial sequences, we need to turn off some the automatics NCBI incorporate when short sequences are detected. Otherwise we'll not be able to see the intended results:
	For this special situation where we BLAST small artificial sequences, we need to turn off some the automatics NCBI incorporate when short sequences are detected. Otherwise we'll not be able to see the intended results:

	In the Google ~~colab~~ we do this inadvertently setting the parameter "<u>short_query=False</u>". In the web browser version this will be analogous as going into the "<u>Algorithm parameters</u>" section (see the screen shot below) in order to gain access to fine-tuning the options, and '''Deselect''' the "<u>Automatically adjust parameters for short input sequences</u>" option.		In the Google Colab we do this inadvertently setting the parameter "<u>short_query=False</u>". In the web browser version this will be analogous as going into the "<u>Algorithm parameters</u>" section (see the screen shot below) in order to gain access to fine-tuning the options, and '''Deselect''' the "<u>Automatically adjust parameters for short input sequences</u>" option.

Carol: /* Random DNA sequences and BLASTN */

2026-09-22T08:35:52Z

Random DNA sequences and BLASTN

← Older revision		Revision as of 09:35, 22 September 2026
Line 239:		Line 239:
	We will now do a BLASTN search using each random sequence as query.		We will now do a BLASTN search using each random sequence as query.

	In Google Colab, this will be analogous to the web browser using the option "blastn" in the section "<u>Program Selection</u>". And in this case we will select "<u>Nucleotide Collection (nr/nt)</u>" as the search database.		In Google Colab, this will be analogous to the web browser using the option "blastn" in the section "<u>Program Selection</u>". And in this case we will select "<u>Nucleotide Collection (nr/nt)</u>" as the search database. In addition we will have to modify the E-value cut-off ("<u>E_VALUE_THRESH</u>") to '''50'''

	'''VERY IMPORTANT''':		'''VERY IMPORTANT''':
Line 245:		Line 245:

	In the Google colab we do this inadvertently setting the parameter "<u>short_query=False</u>". In the web browser version this will be analogous as going into the "<u>Algorithm parameters</u>" section (see the screen shot below) in order to gain access to fine-tuning the options, and '''Deselect''' the "<u>Automatically adjust parameters for short input sequences</u>" option.		In the Google colab we do this inadvertently setting the parameter "<u>short_query=False</u>". In the web browser version this will be analogous as going into the "<u>Algorithm parameters</u>" section (see the screen shot below) in order to gain access to fine-tuning the options, and '''Deselect''' the "<u>Automatically adjust parameters for short input sequences</u>" option.
	~~# Set the E-value cut-off ("<u>Expect threshold</u>") to '''50'''~~

Carol: /* Random DNA sequences and BLASTN */

2026-09-22T08:33:43Z

Random DNA sequences and BLASTN

@@ Line 234: / Line 234: @@
 ===Random DNA sequences and BLASTN===
 Generate 10 random DNA sequence of length 25bp using Google Colab.
@@ Line 275: / Line 255: @@
 :'''QUESTION 2.1''':
 :Answer the following small questions, and '''document your findings''' by pasting in examples of alignments / text snippets from the overview plots generated on google colab:
 :* What is the typical length of the hits (the alignment length)?

Carol: /* Random DNA sequences and BLASTN */

2026-09-22T08:33:21Z

Random DNA sequences and BLASTN

@@ Line 244: / Line 244: @@
 Extend the "<u>Algorithm parameters</u>" section (see the screen shot below) in order to gain access to fine-tuning the options.
 # '''Deselect''' the "<u>Automatically adjust parameters for short input sequences</u>" option.
 # Set the E-value cut-off ("<u>Expect threshold</u>") to '''50'''
@@ Line 254: / Line 275: @@
 :'''QUESTION 2.1''':
 :Answer the following small questions, and '''document your findings''' by pasting in examples of alignments / text snippets from the overview plots generated on google colab:
 :* What is the typical length of the hits (the alignment length)?

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

2026-09-22T08:27:21Z

Part 2.0: Create your first Python Notebook

← Older revision		Revision as of 09:27, 22 September 2026
Line 212:		Line 212:


	==~~Part 2.0:~~ Create your first Python Notebook==		==Create your first Python Notebook==

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

Carol: /* NCBI */

2026-09-22T07:57:58Z

NCBI

← Older revision		Revision as of 08:57, 22 September 2026
Line 514:		Line 514:
	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.

	Blast Job ID: ~~FR65XVA0016~~		'''Blast Job ID: B4D73S06016'''

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

Carol: /* NCBI */

2026-09-22T07:54:38Z

NCBI

← Older revision		Revision as of 08:54, 22 September 2026
Line 500:		Line 500:
	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).

	Blast Job ID: ~~FR6NDFMJ013~~		'''Blast Job ID: B4D0NJAJ016'''

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

Carol: /* BLAST example 2 */

2026-09-22T07:48:54Z

BLAST example 2

← Older revision		Revision as of 08:48, 22 September 2026
Line 442:		Line 442:
	* '''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): ~~DU9XHV8H014~~		'''Blast Job ID (blastn): B4C91VW4016'''

	Blast Job ID (blastp): ~~DU9T4K44014~~		'''Blast Job ID (blastp): B4CMGVXT016'''

Carol: /* Links */

2026-09-22T06:26:30Z

Links

← Older revision		Revision as of 07:26, 22 September 2026
Line 187:		Line 187:

	===Links===		===Links===
	* A few notes on how to use a [https://colab.research.google.com/notebooks/basic_features_overview.ipynb#scrollTo=WUtu4316QSHL Google Colab]		A few notes on how to use a [https://colab.research.google.com/notebooks/basic_features_overview.ipynb#scrollTo=WUtu4316QSHL Google Colab]

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