22111 - Recent changes [en]

BLOSUM matrix examples

Henni — Tue, 22 Sep 2026 14:42:04 GMT

BLOSUM 30

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 ==BLOSUM 30==
 <pre>
     A  B  C  D  E  F  G  H  I  K  L  M  N  P  Q  R  S  T  V  W  X  Y  Z  *
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 * -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7  1
 </pre>
 ==BLOSUM 62==

ExPairwiseAlignment-AnswersEng

Henni — Tue, 22 Sep 2026 13:57:57 GMT

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	* The exercise itself is here: [[ExPairwiseAlignment]]		* The exercise itself is here: [[ExPairwiseAlignment]]
	* The Danish version of the answers is here: [[ExPairwiseAlignment-Answers]]		<!-- * The Danish version of the answers is here: [[ExPairwiseAlignment-Answers]] -->

	== Part 0==		== Part 0==

Exercise:BLAST new

Carol — Tue, 22 Sep 2026 08:57:59 GMT

Random protein sequences and BLASTP

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	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?

ExBlast-Answers new

Carol — Tue, 22 Sep 2026 08:48:16 GMT

QUESTION 2.3

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	-->		-->
	*''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?'':
	:Typically 15-22. Rarely gaps, but several mismatches.		:Typically 15-23. Rarely gaps, but several mismatches.

	*''What is the range of E-values?'':		*''What is the range of E-values?'':
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	*''Try to inspect a few of the alignments in details ("+" means similar) - do you find any that look plausible, if we for a moment ignore the length/E-value?''		*''Try to inspect a few of the alignments in details ("+" means similar) - do you find any that look plausible, if we for a moment ignore the length/E-value?''
	:Yes, maybe. See ''e.g.'' the alignment below, it has 77% identities (but it is way too short to be significant, as the E-value tells us).		:Yes, maybe. See ''e.g.'' the alignment below, it has 56.5% identities (but it is way too short to be significant, as the E-value tells us).

			Generating Random Sequence 1 for BLAST...
			DTGVHDAQEIGITCQFQPVCFLFSP
	**Alignment** 1		**Alignment** 1
	Title: ref\|~~WP_179589105~~.1\| ~~non-ribosomal peptide~~ synthetase [~~Pigmentiphaga litoralis~~] >gb\|~~NYE25977~~.1\| ~~amino acid adenylation domain-containing protein~~ [~~Pigmentiphaga litoralis] >gb\|NYE85097~~.~~1\| amino acid adenylation domain~~- ~~containing protein [Pigmentiphaga litoralis~~]		Title: ref\|WP_243336483.1\| class III lanthionine synthetase LanKC [Streptomyces sp. AP-93] >gb\|MCJ0871799.1\| class III lanthionine synthetase LanKC [Streptomyces sp. AP-93]
	Accession: ~~WP_179589105~~		Accession: WP_243336483
	Length: ~~1782~~		Length: 827
	Max Score: 67.0		Max Score: 69.0
	Bits: 30.~~4166~~		Bits: 31.187
	Identities: 8		Identities: 13
	Align_length: 22		Align_length: 23
	Gaps: 0		Gaps: 0
	%Ident: 36.36 %		%Ident: 56.52 %
	Query Cover: 88 %		Query Cover: 92 %
	E value: 1.~~25e~~+02		E value: 1.12e+02
	~~LTNNVNMHWTLPYTVSHVYVNP~~		Query: TGVHDAQEIGITCQFQPVCFLFS
	~~L ++ HW~~ +P+~~T+SH++ +P~~		Match: T VHDA I +T QF P C LF+
	~~LAARISQHWCVPFTISHIFDHP~~		Subject: TAVHDALLIDLTSQFHPACGLFT

Exercise:BLAST new

Carol — Tue, 22 Sep 2026 08:36:24 GMT

Random DNA sequences and BLASTN

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	===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;">
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	==~~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]
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	Generate 10 random DNA sequence of length 25bp using Google Colab.		Generate 10 random DNA sequence of length 25bp using Google Colab.

	We will now do a BLASTN search using ~~the~~ random sequence as query~~. Select the option "blastn" in the section "<u>Program Selection</u>". Choose "<u>Nucleotide Collection (nr/nt)</u>" as the search database~~.		We will now do a BLASTN search using each random sequence as query.

	'''~~VERY IMPORTANT~~''':		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'''
	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:
			'''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:

			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.

	~~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'''~~


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	[[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 Q2.2)''		:''(Remember to '''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?
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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): ~~DU9XHV8H014~~		'''Blast Job ID (blastn): B4C91VW4016'''

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


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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).

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

	[[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.

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

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

ExBlast-Answers new

Carol — Mon, 21 Sep 2026 16:36:27 GMT

QUESTION 2.1

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	===QUESTION 2.1===		===QUESTION 2.1===

	~~:There will typically be several 100% identity hits, ''e.g.'':~~

	**Alignment** 1		**Alignment** 1
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	*''What is the typical length of the hits (the alignment length)?'':		*''What is the typical length of the hits (the alignment length)?'':
	:Typically around 17-22 base pairs.		:Typically around 17-24 base pairs.

	*''What is the typical % identity?'':		*''What is the typical % identity?'':
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	*''In what range are the bit-scores ("max score)?'':		*''In what range are the bit-scores ("max score)?'':
	:typically 30-40 bits.		:typically 30-45 bits.

	*''What is the range of the E-values?'':		*''What is the range of the E-values?'':
	:1~~.88e+00~~ - ~~2.29e+01~~		:1-15
	:usually varying from 1 to 50 (occasionally, you might find hits as "good" as 0.1).		:usually varying from 1 to 50 (occasionally, you might find hits as "good" as 0.1).
	:'''Note''': we ~~chose~~ to use an E-value threshold of 50.0. ~~The~~ default is 0.05.		:'''Note''' that here we choose to use an E-value threshold of 50.0 as a cut-off. That means that some sequences do not give an output if the E-value of the best alignment is higher than that. Also note that when running BLAST to identify homologous sequences the default cut-off is 0.05.

	===QUESTION 2.2===		===QUESTION 2.2===

Exercise:BLAST new

Carol — Mon, 21 Sep 2026 16:14:30 GMT

Random protein sequences and BLASTP

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	==Part 2: Assessing the statistical significance of BLAST hits==		==Part 2: Assessing the statistical significance of BLAST hits==
	~~<div style="background-color: lavender; border: solid thin grey;">~~
	~~:'''IMPORTANT:''' Limit your search to "bacteria" (taxid: 2) in ALL of this section (PART 2) to make the BLAST searches run quicker.~~
	~~</div>~~

	As discussed in the lecture, there will be a risk of getting false positive results (hits to sequences that are not related to our input sequence) by purely stochastic means. In this first part of the exercise, we will be investigating this further, by examining what happens when we submit randomly generated sequences to BLAST searches.		As discussed in the lecture, there will be a risk of getting false positive results (hits to sequences that are not related to our input sequence) by purely stochastic means. In this first part of the exercise, we will be investigating this further, by examining what happens when we submit randomly generated sequences to BLAST searches.
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	===Random DNA sequences and BLASTN===		===Random DNA sequences and BLASTN===

	*Generate 10 random DNA sequence of length 25bp using Google Colab		Generate 10 random DNA sequence of length 25bp using Google Colab.

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

	We will now do a BLASTN search using the random sequence as query. Select the option "blastn" in the section "<u>Program Selection</u>". Choose "<u>Nucleotide Collection (nr/nt)</u>" as the search database.		We will now do a BLASTN search using the random sequence as query. Select the option "blastn" in the section "<u>Program Selection</u>". Choose "<u>Nucleotide Collection (nr/nt)</u>" as the search database.
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	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:

	* Extend the "<u>Algorithm parameters</u>" section (see the screen shot below) in order to gain access to fine-tuning the options.		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.		# '''Deselect''' the "<u>Automatically adjust parameters for short input sequences</u>" option.
	*# Set the E-value cut-off ("<u>Expect threshold</u>") to '''50'''		# Set the E-value cut-off ("<u>Expect threshold</u>") to '''50'''


	[[file:Blastn_cropped+circle.png‎\|center\|frame\|'''Remember to adjust the BLAST settings''']]		[[file:Blastn_cropped+circle.png‎\|center\|frame\|'''Remember to adjust the BLAST settings''']]

	* Inspect the results.		Inspect the results.


			[[Image:Office-notes-line_drawing.png\|30px\|left]]
	:'''QUESTION 2.1''':		:'''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:		: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:
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	:* What is the range of the E-values?		:* What is the range of the E-values?

			[[Image:Office-notes-line_drawing.png\|30px\|left]]
	:'''QUESTION 2.2''':		:'''QUESTION 2.2''':
	:*What is the '''biological''' significance of these hits / is there any biological meaning?		:What is the '''biological''' significance of these hits / is there any biological meaning?

	===Random protein sequences and BLASTP===		===Random protein sequences and BLASTP===
	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.		:'''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.
	* '''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).		:'''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).


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

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


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	[[Image:Office-notes-line_drawing.png\|30px\|left]]		[[Image:Office-notes-line_drawing.png\|30px\|left]]
	:'''QUESTION 2.4''':		:'''QUESTION 2.4''':
	:* 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.

22111:Course plan autumn 2026

Carol — Mon, 21 Sep 2026 14:16:41 GMT

Tuesday Sep 22 — BLAST

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	=== Tuesday Sep 22 — BLAST ===		=== Tuesday Sep 22 — BLAST ===
	:'''Lecture:''' ''Introduction to BLAST'' — Carolina Barra Quaglia.		:'''Lecture:''' ''Introduction to BLAST'' — Carolina Barra Quaglia.
	:'''Curriculum:''' ~~section 3.2.5 → 3.3 (i.e. pages 47-52) in Immunological Bioinformatics (PDF:~~ on DTU Learn).		:'''Curriculum:''' on DTU Learn.
	:'''Slides:''' on DTU Learn.		:'''Slides:''' on DTU Learn.
	:'''Exercise: [[Exercise:~~_BLAST3~~\|BLAST]]'''		:'''Exercise: [[Exercise:BLAST_new\|BLAST]]'''
	<!--		<!--
	:'''Extra material:'''		:'''Extra material:'''

ExBlast-Answers new

Carol — Mon, 21 Sep 2026 14:01:00 GMT

QUESTION 1.6

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	==Part 1: Your first BLAST search==		==Part 1: Your first BLAST search==

			===QUESTION 1.1===
			The main difference is that core_nt excludes most eukaryotic chromosome sequences, making it smaller and faster than nr/nt, so NCBI uses it as the default for more efficient searches.

	===QUESTION 1.2===		===QUESTION 1.2===
			* ''Which database did you use?''
			:core_nt
	* ''what is the identifier (Accession)?''		* ''what is the identifier (Accession)?''
	:~~OL351605 or M57671~~ (Note that the latter was also part of the sequence name for your query sequence!)		:J00336.1 (Note that the latter was also part of the sequence name for your query sequence!)
	* ''what is the alignment score ("Max score in bits")?''		* ''what is the alignment score ("Max score in bits")?''
	:The max score is ~~780~~ bits ~~(Raw score is 864)~~		:The max score is 708 bits
	* ''what is the percent identity and query coverage?''		* ''what is the percent identity and query coverage?''
	:100%		:100% and 100%
	* ''what is the E-value?''		* ''what is the E-value?''
	:0.0 (actually, a number so small that it is rounded off to 0.0)		:0.0 (actually, a number so small that it is rounded off to 0.0)
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	:No, of course not, since the sequences are identical		:No, of course not, since the sequences are identical

	===QUESTION 1.2===		===QUESTION 1.3===
			* ''Which database did you use?''
			:core_nt
	* ''what is the identifier (Accession)?''		* ''what is the identifier (Accession)?''
	:~~MT335691~~.~~1 or MT335690.1 or MT335689.1, they have the same score and are therefore equally good~~		:NM_000207.3
	* ''what is the alignment score ("max score")?''		* ''what is the alignment score ("max score")?''
	:~~205~~		:603
	* ''what is the percent identity and query coverage?''		* ''what is the percent identity and query coverage?''
	:identity: 74.49% and query coverage: 76%		:identity: 94.34% and query coverage: 99%
	* ''what is the E-value?''		* ''what is the E-value?''
	:2e-47 (meaning 2×10<sup>-48</sup>)		:7e-168 (meaning 7×10<sup>-168</sup>)
	* ''are there any gaps in the alignment?''		* ''are there any gaps in the alignment?''
	:~~Yes, there are five gaps in the query sequence and two gaps in the database sequence, totaling 15 positions.~~		:No

	===QUESTION 1.3===		===QUESTION 1.4===
			* ''Which database did you use?''
			:Human G+T (2 databases)
	* ''what is the identifier (Accession)?''		* ''what is the identifier (Accession)?''
	:~~NM_001185098 or NM_001185097 or~~ NM_000207, they have the same score and are therefore equally good. Note that these are among the equally good hits found in the previous question.		:NM_000207.3, they have the same score and are therefore equally good. Note that these are among the equally good hits found in the previous question.
	* ''what is the alignment score ("max score")?''		* ''what is the alignment score ("max score")?''
	:~~205~~		:603
	* ''what is the percent identity and query coverage?''		* ''what is the percent identity and query coverage?''
	:identity: 74.49% and query coverage: 76%		:identity: 94.34% and query coverage: 99%
	* ''what is the E-value?''		* ''what is the E-value?''
	:3e-50 (meaning 3×10<sup>-50</sup>)		:3e-170 (meaning 3×10<sup>-170</sup>)
	* ''are there any gaps in the alignment?''		* ''are there any gaps in the alignment?''
	:~~Yes, there are exactly the same gaps as in the previous question.~~		:No

	===QUESTION 1.4===		===QUESTION 1.5===
	''What are the sizes (in basepairs) of the databases we used for the two BLAST searches?''		''What are the sizes (in basepairs) of the databases we used for the two BLAST searches?''

	nt(Human): 2,933,~~612,979~~,~~911~~ letters (= basepairs), Human G+T: 4,017,001,775 letters (= basepairs).		nt(Human): 1,081,933,534,067 letters (= basepairs), Human G+T: 4,017,001,775 letters (= basepairs).

	===QUESTION 1.5===		===QUESTION 1.6===

	*''What is the ratio between the database sizes in the two BLAST searches?''		*''What is the ratio between the database sizes in the two BLAST searches?''
	: 2,933,~~612,979~~,~~911~~ / 4,017,001,775 = <u>~~730~~</u>		: 1,081,933,534,067 / 4,017,001,775 = <u>~269</u>
	*''What is the ratio between the E-values (for the best human hits) in the two BLAST searches? ''		*''What is the ratio between the E-values (for the best human hits) in the two BLAST searches? ''
	:2e-47 / 3e-50 = <u>~~666~~</u>		:7e-168 / 3e-170 = <u>~233</u>
	:Note: since the E-values have only three significant digits, you cannot expect to get the exact same result.		:Note: since the E-values have only three significant digits, you cannot expect to get the exact same result.
	:Also note, you can google "2e-47 / 3e-50" directly and the answer will show up in the results.		:Also note, you can google "7e-168 / 3e-170" directly and the answer will show up in the results.
	*''What is the relationship between database size and E-value for hits with identical alignment score?''		*''What is the relationship between database size and E-value for hits with identical alignment score?''
	:The E-value is directly proportional to the database size.		:The E-value is directly proportional to the database size.
	:Note: Conceptually this ~~is easy to understand - getting~~ an alignment ~~with~~ the given score (~~205~~ bits) is more SIGNIFICANT in the smaller database. In larger database there is a larger chance of randomly picking up matches.		:Note: Conceptually this means that an alignment within the given score (603 bits) is more SIGNIFICANT in the smaller database. In larger database there is a larger chance of randomly picking up matches.
	*''In conclusion: if the database size is doubled, what will happen to the E-value?''		*''In conclusion: if the database size is doubled, what will happen to the E-value?''
	:Each time the database size doubles, the E-value doubles as well.		:Each time the database size doubles, the E-value doubles as well.

ExBlast-Answers new

Carol — Mon, 21 Sep 2026 13:43:36 GMT

Created page with "Answers to the BLAST exercise. Values for database sizes etc. retrieved September 21, 2026 ==Part 1: Your first BLAST search== ===QUESTION 1.2=== * ''what is the identifier (Accession)?'' :OL351605 or M57671 (Note that the latter was also part of the sequence name for your query sequence!) * ''what is the alignment score ("Max score in bits")?'' :The max score is 780 bits (Raw score is 864) * ''what is the percent identity and query coverage?'' :100% * ''what is the E..."

New page

Answers to the BLAST exercise. Values for database sizes etc. retrieved
September 21, 2026

==Part 1: Your first BLAST search==

===QUESTION 1.2===
* ''what is the identifier (Accession)?''
:OL351605 or M57671 (Note that the latter was also part of the sequence name for your query sequence!)
* ''what is the alignment score ("Max score in bits")?''
:The max score is 780 bits (Raw score is 864)
* ''what is the percent identity and query coverage?''
:100%
* ''what is the E-value?''
:0.0 (actually, a number so small that it is rounded off to 0.0)
* ''are there any gaps in the alignment?''
:No, of course not, since the sequences are identical

===QUESTION 1.2===
* ''what is the identifier (Accession)?''
:MT335691.1 or MT335690.1 or MT335689.1, they have the same score and are therefore equally good
* ''what is the alignment score ("max score")?''
:205
* ''what is the percent identity and query coverage?''
:identity: 74.49% and query coverage: 76%
* ''what is the E-value?''
:2e-47 (meaning 2×10-48)
* ''are there any gaps in the alignment?''
:Yes, there are five gaps in the query sequence and two gaps in the database sequence, totaling 15 positions.

===QUESTION 1.3===
* ''what is the identifier (Accession)?''
:NM_001185098 or NM_001185097 or NM_000207, they have the same score and are therefore equally good. Note that these are among the equally good hits found in the previous question.
* ''what is the alignment score ("max score")?''
:205
* ''what is the percent identity and query coverage?''
:identity: 74.49% and query coverage: 76%
* ''what is the E-value?''
:3e-50 (meaning 3×10-50)
* ''are there any gaps in the alignment?''
:Yes, there are exactly the same gaps as in the previous question.

===QUESTION 1.4===
''What are the sizes (in basepairs) of the databases we used for the two BLAST searches?''

nt(Human): 2,933,612,979,911 letters (= basepairs), Human G+T: 4,017,001,775 letters (= basepairs).

===QUESTION 1.5===

*''What is the ratio between the database sizes in the two BLAST searches?''
: 2,933,612,979,911 / 4,017,001,775 = 730
*''What is the ratio between the E-values (for the best human hits) in the two BLAST searches? ''
:2e-47 / 3e-50 = 666
:Note: since the E-values have only three significant digits, you cannot expect to get the exact same result.
:Also note, you can google "2e-47 / 3e-50" directly and the answer will show up in the results.
*''What is the relationship between database size and E-value for hits with identical alignment score?''
:The E-value is directly proportional to the database size.
:Note: Conceptually this is easy to understand - getting an alignment with the given score (205 bits) is more SIGNIFICANT in the smaller database. In larger database there is a larger chance of randomly picking up matches.
*''In conclusion: if the database size is doubled, what will happen to the E-value?''
:Each time the database size doubles, the E-value doubles as well.

==Part 2: Assessing the statistical significance of BLAST hits==

===QUESTION 2.1===

:There will typically be several 100% identity hits, ''e.g.'':

****Alignment**** 1
Title: gi|2440392781|emb|OX421481.1| Eilema caniola genome assembly, chromosome: 20
Accession: OX421481
Length: 22119023
Max Score: 44.0
Bits: 40.9604
Identities: 22
Align_length: 22
Gaps: 0
%Ident: 100.00 %
Query Cover: 88 %
E value: 1.88e+00
TTCTGAAAGGTCCTCTCGATAC
||||||||||||||||||||||
TTCTGAAAGGTCCTCTCGATAC

*''What is the typical length of the hits (the alignment length)?'':
:Typically around 17-22 base pairs.

*''What is the typical % identity?'':
:90% - 100%

*''In what range are the bit-scores ("max score)?'':
:typically 30-40 bits.

*''What is the range of the E-values?'':
:1.88e+00 - 2.29e+01
:usually varying from 1 to 50 (occasionally, you might find hits as "good" as 0.1).
:'''Note''': we chose to use an E-value threshold of 50.0. The default is 0.05.

===QUESTION 2.2===
''What is the biological significance of the hits you found / is there any biological meaning?'':

This makes absolutely NO biological sense(!) The hits are real enough as such, they represent sequences that actually are in the database. But we know that our query sequences are completely random and therefore have no evolutionary relationship with the hits. The only reason we found our hits is that the database is so vast that we for for purely stochastic reasons happen upon sequences that are similar.

The E-values tell us precisely this: As described in the BLAST lecture, the alignment score will follow an extreme value distribution for those sequences that are not related to our query sequences, and the E-value is ''the expected number'' of spurious (unrelated) hits with the given alignment score or better, given the database size.

'''Note:''' Don't be confused by the difference between alignment score and bit score; bit score is simply the alignment score normalized by a constant factor which gives a result expressible in bits.

===QUESTION 2.3===


*''What is the typical length of the alignment and do they contain gaps?'':
:Typically 15-22. Rarely gaps, but several mismatches.

*''What is the range of E-values?'':
:Typically 100-1000

*''Try to inspect a few of the alignments in details ("+" means similar) - do you find any that look plausible, if we for a moment ignore the length/E-value?''
:Yes, maybe. See ''e.g.'' the alignment below, it has 77% identities (but it is way too short to be significant, as the E-value tells us).

****Alignment**** 1
Title: ref|WP_179589105.1| non-ribosomal peptide synthetase [Pigmentiphaga litoralis] >gb|NYE25977.1| amino acid adenylation domain-containing protein [Pigmentiphaga litoralis] >gb|NYE85097.1| amino acid adenylation domain- containing protein [Pigmentiphaga litoralis]
Accession: WP_179589105
Length: 1782
Max Score: 67.0
Bits: 30.4166
Identities: 8
Align_length: 22
Gaps: 0
%Ident: 36.36 %
Query Cover: 88 %
E value: 1.25e+02
LTNNVNMHWTLPYTVSHVYVNP
L ++ HW +P+T+SH++ +P
LAARISQHWCVPFTISHIFDHP

*''If we had used the default E-value cutoff of 10 would any hits have been found?'':
:No (note: the default is actually 0.05 now). Note the difference from the nucleotide database searches (whose E-values were typically in the range 1-50): if we had run BLASTN with an E-value threshold of 1000, we would have had many pages of hits for each query sequence.

===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)?'':
:The risk of getting a false hit (an unrelated sequence with a "decent" E-value) is much larger when working with DNA sequences. Remember than we used 50 as E-value cut-off for BLASTN, while we used 1000 with BLASTP in order to see any hits at all.

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



*''Do we find any significant hits? (E-value?)'':
:Yes, a lot. The first many hits have an E-value of 0.0, and hit #100 is still very significant (3e-98) — note that by default, only the top 100 hits are shown!

*''Are all the best hits the same category of enzymes?'':
:Yes, they are alkaline proteases (except a few that are hypothetical proteins).
:Note that you can click the Accession code for a hit and go directly to the corresponding entry in the database.

*''From what you have seen, what is best for identifying intermediate quality hits - DNA or Protein BLAST?'':
:Protein BLAST (BLASTP). If you have very high quality hits, they can be identified by both methods, but if the evolutionary distance is larger, BLASTP is clearly better.
:Note: Recall from the PyMOL exercises that information between distant genes/proteins are conserved from: Structure > Peptide Sequence > Nucleotide sequence. So when the evolutionary distance is larger, blastp would generally give better hits than blastn.

-->

===QUESTION 3.1===
'''STEP 1 - cleaning up the sequence: '''

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

>CLONE12
AACGGGCACGGGACGCATGTAGCTGGAACAGTGGCAGCCGTAAATAATAATGGTATCGGA
GTTGCCGGGGTTGCAGGAGGAAACGGCTCTACCAATAGTGGAGCAAGGTTAATGTCCACA
CAAATTTTTAATAGTGATGGGGATTATACAAATAGCGAAACTCTTGTGTACAGAGCCATT
GTTTATGGTGCAGATAACGGAGCTGTGATCTCGCAAAATAGCTGGGGTAGTCAGTCTCTG
ACTATTAAGGAGTTGCAGAAAGCTGCGATCGACTATTTCATTGATTATGCAGGAATGGAC
GAAACAGGAGAAATACAGACAGGCCCTATGAGGGGAGGTATATTTATAGCTGCCGCCGGA
AACGATAACGTTTCCACTCCAAATATGCCTTCAGCTTATGAACGGGTTTTAGCTGTGGCC
TCAATGGGACCAGATTTTACTAAGGCAAGCTATAGCACTTTTGGAACATGGACTGATATT
ACTGCTCCTGGCGGAGATATTGACAAATTTGATTTGTCAGAATACGGAGTTCTCAGCACT
TATGCCGATAATTATTATGCTTATGGAGAGGGAACATCCATGGCTTGTCCACATGTCGCC
GGCGCCGCC

'''STEP 2 - thinking about the task: '''

*''Subquestion: Give a summary of your considerations.''
**''Based on the information given: is the sequence protein-coding? ''
::Yes — we know this because the PCR primers used to clone the sequence target '''known enzymes'''. Therefore, it will make sense to try to translate the sequence using Virtual Ribosome.
:*''If it is, can you trust it will contain both a START and STOP codon? ''
::No — the PCR primers used to clone the sequence target '''the middle of the sequence''', in other words we must assume that our sequence is a fragment. Therefore, the ORF finder in Virtual Ribosome should be set to Start codon: None.
:*''Do we know if the sequence is sense or anti-sense? ''
::No — the PCR process amplifies a stretch of double-stranded DNA. Therefore, we should let Virtual Ribosome search in '''all 6 reading frames'''.

'''STEP 3 - Performing the database search''':
We want to use BLAST to search the large databases. Let's therefore try the following:
# BLASTN
# Translate to protein (using Virtual Ribosome).
# BLASTP
Both when doing BLASTN and BLASTP we will use the NR database in order to search as broadly as possible. It would not make sense to use an organism-specific database when we don't know which organism our sequence stems from.

1) BLASTN. When trying BLASTN against NR we get some borderline significant results, but observe how small the query coverage percentages are (check also the Graphic Summary tab!).

[[image:NCBI BlastN_CLONE12 new_version.png]]
[[image:NCBI BlastN_CLONE12 Graphic Summary.png]]

There is simply nothing in the entire NR database that has enough similarity to our whole query sequence. A search on the DNA level is only suited for finding very close hits.

2) Translate using Virtual Ribosome with the settings we chose under Step 2 above.

The result from the ORF finder:

VIRTUAL RIBOSOME
----------------
Translation table: Standard SGC0

>CLONE12_rframe1_ORF
Reading frame: 1

N G H G T H V A G T V A A V N N N G I G V A G V A G G N G S
5' AACGGGCACGGGACGCATGTAGCTGGAACAGTGGCAGCCGTAAATAATAATGGTATCGGAGTTGCCGGGGTTGCAGGAGGAAACGGCTCT 90
..........................................................................................

T N S G A R L M S T Q I F N S D G D Y T N S E T L V Y R A I
5' ACCAATAGTGGAGCAAGGTTAATGTCCACACAAATTTTTAATAGTGATGGGGATTATACAAATAGCGAAACTCTTGTGTACAGAGCCATT 180
.....................>>>..................................................................

V Y G A D N G A V I S Q N S W G S Q S L T I K E L Q K A A I
5' GTTTATGGTGCAGATAACGGAGCTGTGATCTCGCAAAATAGCTGGGGTAGTCAGTCTCTGACTATTAAGGAGTTGCAGAAAGCTGCGATC 270
.........................................................)))............)))...............

D Y F I D Y A G M D E T G E I Q T G P M R G G I F I A A A G
5' GACTATTTCATTGATTATGCAGGAATGGACGAAACAGGAGAAATACAGACAGGCCCTATGAGGGGAGGTATATTTATAGCTGCCGCCGGA 360
........................>>>..............................>>>..............................

N D N V S T P N M P S A Y E R V L A V A S M G P D F T K A S
5' AACGATAACGTTTCCACTCCAAATATGCCTTCAGCTTATGAACGGGTTTTAGCTGTGGCCTCAATGGGACCAGATTTTACTAAGGCAAGC 450
........................>>>....................................>>>........................

Y S T F G T W T D I T A P G G D I D K F D L S E Y G V L S T
5' TATAGCACTTTTGGAACATGGACTGATATTACTGCTCCTGGCGGAGATATTGACAAATTTGATTTGTCAGAATACGGAGTTCTCAGCACT 540
...............................................................)))........................

Y A D N Y Y A Y G E G T S M A C P H V A G A A
5' TATGCCGATAATTATTATGCTTATGGAGAGGGAACATCCATGGCTTGTCCACATGTCGCCGGCGCCGCC 609
.......................................>>>...........................

('''Tip:''' Remember that you can get the sequence in FASTA format via the FASTA link on the result page):

>CLONE12_rframe1_ORF
NGHGTHVAGTVAAVNNNGIGVAGVAGGNGSTNSGARLMSTQIFNSDGDYTNSETLVYRAI
VYGADNGAVISQNSWGSQSLTIKELQKAAIDYFIDYAGMDETGEIQTGPMRGGIFIAAAG
NDNVSTPNMPSAYERVLAVASMGPDFTKASYSTFGTWTDITAPGGDIDKFDLSEYGVLST
YADNYYAYGEGTSMACPHVAGAA

3) BLASTP



We get several very significant hits. When looking at the top hits and disregarding "hypothetical" and "uncharacterized" proteins, we can see that the rest are almost all serine proteases. Some of them are described as belonging to the of the S8 family.

[[image:NCBI BlastP_CLONE12_rframe1_ORF new version.png]]

Let's take a closer look at the first hit that is not "uncharacterized":
[[image:NCBI_BlastP_CLONE12_best_hit.png]]

Note that although it is not a perfect hit (our query sequence not existing in the database) it looks reasonable: the alignment covers a large part of the query with Identity of 54% and Similarity (Positives) of 69%.

Taken together with the fact that almost all the best non-hypothetical hits are serine proteases, we have a very strong indication that our mystery sequence, CLONE12, is a peptidase or protease of the S8 family.

==Part 4: BLAST'ing Genomes==

===QUESTION 4.1===
''What information is given about the relationship between this gene and the gene "HTA1"?''

They are nearly identical ("one of two nearly identical (see also HTA1) subtypes").

Protein sequence:
>YBL003C
MSGGKGGKAGSAAKASQSRSAKAGLTFPVGRVHRLLRRGNYAQRIGSGAPVYLTAVLEYL
AAEILELAGNAARDNKKTRIIPRHLQLAIRNDDELNKLLGNVTIAQGGVLPNIHQNLLPK
KSAKTAKASQEL*

===QUESTION 4.2===
*''How many high-confidence hits do we get?'':
:3 — HTA1, HTA2 and HTZ1.
:Note: If you click on the Gene links for the two top hits, you will see that one is HTA1 and the other is HTA2.

*''Do the hits make sense, from what you have read about HTA2 at the SGD webpage?'':
:Yes; HTA1 and HTA2 are indeed nearly identical (only 2 amino acids differ).

===QUESTION 4.3===

*''How many high-confidence hits (with E-value better than 10-10) are found?''
:Answer: 29.

Exercise:BLAST new

Carol — Mon, 21 Sep 2026 13:41:40 GMT

Introduction

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	<div style="background-color: lavender; border: solid thin grey;">		<div style="background-color: lavender; border: solid thin grey;">
	:'''IMPORTANT:''' BLAST is a quite computationally intensive algorithm, and we have in recent years run into issues with overburdening the NCBI server, with 150+ students submitting jobs at the same time from the same DTU IP address. We have therefore implemented a few optimization/workarounds, that it is '''important you remember to follow'''. In some of the sections below, you will be asked to limit your search to a certain subset of the BLAST database (e.g. only search in the "bacterial" part of the NR database). This will limit the amount of data to search through and will make the search finish faster.		:'''IMPORTANT:''' BLAST is a quite computationally intensive algorithm, and we have in recent years run into issues with overburdening the NCBI server, with 150+ students submitting jobs at the same time from the same DTU IP address. We have therefore implemented a few optimization/workarounds.

	~~[[Image~~:~~BLAST_limit_search~~.~~png\|center\|600px\|border]]~~		:If you still experience long waiting times you can try an alternative internet connection, such as a mobile hotspot. Alternatively, you can copy the pre-saved searches under '''Blast Job ID:XXX''' and use them on the link from BLAST called '''Saved Strategies'''. Please notice that these links will only work for the duration of the exercise session.

			[[Image:BLAST_Saved_Strategies.png\|center\|600px\|border]]
	:'''NOTE: if you still experience long waiting times you can try an alternative internet connection, such as a mobile hotspot. Alternatively, you can click on the provided links to get the expected output. Please notice that these links will only work for the duration of the exercise session.~~'''~~

File:BLAST Saved Strategies.png

Carol — Mon, 21 Sep 2026 13:37:13 GMT

Carol uploaded File:BLAST Saved Strategies.png

New page

Exercise:BLAST new

Carol — Mon, 21 Sep 2026 13:34:28 GMT

Concerning database size and E-values

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	==Part 1: Your first BLAST search==		==Part 1: Your first BLAST search==

	Below is the mRNA sequence for insulin from ~~our closest~~ relative, the common ~~chimpanzee~~ (''~~Pan troglodytes~~'').		Below is the mRNA sequence for insulin from a close relative, the common macaque (''Macaca fascicularis'').

	>~~NM_001008996~~.~~2 Pan troglodytes insulin~~ (~~INS~~), ~~mRNA~~		>J00336.1 Monkey (M. fascicularis) preproinsulin mRNA, complete cds
	~~AGCCCTCCAGGACAGGCTGCATCAGAAGAGGCCATCAAGCAGATCACTGTCCTTCTGCCATGGCCCTGTG~~		AACCCTCCGGGACAGGCTGCATCAGAAGAGGTCAGCAAGCAGGTCACTGTCCTTCGGCTATGGCCCTGTG
	~~GATGCGCCTCCTGCCCCTGCTGGTGCTGCTGGCCCTCTGGGGACCTGACCCAGCCTCGGCCTTTGTGAAC~~		GATGCGCCTCCTGCCCCTGCTGGCGCTGCTGGCCCTCTGGGGACCTGACCCGGCCCCGGCCTTTGTGAAC
	~~CAACACCTGTGCGGCTCCCACCTGGTGGAAGCTCTCTACCTAGTGTGCGGGGAACGAGGCTTCTTCTACA~~		CAGCACCTGTGCGGCTCCCACCTAGTGGAAGCTCTCTACCTGGTGTGCGGGGAACGAGGCTTCTTCTACA
	~~CACCCAAGACCCGCCGGGAGGCAGAGGACCTGCAGGTGGGGCAGGTGGAGCTGGGCGGGGGCCCTGGTGC~~		CACCCAAGACCCGCCGGGAGGCAGAGGACCCTCAGGTGGGGCAGGTGGAGCTGGGCGGGGGCCCTGGCGC
	~~AGGCAGCCTGCAGCCCTTGGCCCTGGAGGGGTCCCTGCAGAAGCGTGGTATCGTGGAACAATGCTGTACC~~		AGGCAGCCTGCAGCCCTTGGCGCTGGAGGGGTCCCTGCAGAAGCGCGGCATCGTGGAGCAGTGCTGCACC
	~~AGCATCTGCTCCCTCTACCAGCTGGAGAACTACTGCAACTAGATGGAATAAAGCCCTTGAACCAGC~~		AGCATCTGCTCCCTCTACCAGCTGGAGAACTACTGCAACTAA

	We will use BLAST to determine whether this sequence looks like the human mRNA for insulin. There are two ways we can do this:		We will use BLAST to determine whether this sequence looks like the human mRNA for insulin. There are two ways we can do this:
Line 104:		Line 104:


	'''Blast Job ID: ~~XXX~~'''		'''Blast Job ID: B2C1HZPV014'''
	<!--		<!--
	:* Which database did you use? core_nt		:* Which database did you use? core_nt
	:* What is the identifier (Accession)? ~~NM_001008996~~.2		:* What is the identifier (Accession)? J00336.1
	:* What is the alignment score ("max score")? ~~751~~		:* What is the alignment score ("max score")? 708
	:* What is the percent identity and query coverage? 100%		:* What is the percent identity and query coverage? 100% and 100%
	:* What is the E-value? 0		:* What is the E-value? 0
	:* Are there any gaps in the alignment? No		:* Are there any gaps in the alignment? No
Line 117:		Line 117:

	[[Image:Office-notes-line_drawing.png\|30px\|left]]		[[Image:Office-notes-line_drawing.png\|30px\|left]]
	:'''QUESTION 1.2''':		:'''QUESTION 1.3''':

	:Answer the same questions as before about the hit you found now.		:Answer the same questions as before about the human hit you found now.
			<!--
			:* Which database did you use? core_nt
			:* What is the identifier (Accession)? NM_000207.3
			:* What is the alignment score ("max score")? 603
			:* What is the percent identity and query coverage? 94.34% and 99%
			:* What is the E-value? 7e-168
			:* Are there any gaps in the alignment? No
			-->

	=== Search against Human G+T ===		=== Search against Human G+T ===
Line 130:		Line 138:

	[[Image:Office-notes-line_drawing.png\|30px\|left]]		[[Image:Office-notes-line_drawing.png\|30px\|left]]
	:'''QUESTION 1.3''':		:'''QUESTION 1.4''':
	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: ~~DU93YZB1014~~		'''Blast Job ID: B2CCWWRV014'''

			<!--
			:* Which database did you use? Human G+T (2 databases)
			:* What is the identifier (Accession)? NM_000207.3
			:* What is the alignment score ("max score")? 603
			:* What is the percent identity and query coverage? 94.34% and 99%
			:* What is the E-value? 3e-170
			:* Are there any gaps in the alignment? No
			-->

	===Concerning database size and E-values===		===Concerning database size and E-values===
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	[[Image:Office-notes-line_drawing.png\|30px\|left]]		[[Image:Office-notes-line_drawing.png\|30px\|left]]
	:'''QUESTION 1.4''':		:'''QUESTION 1.5''':
	What are the sizes (in basepairs) of the databases we used for the two BLAST searches? ('''Tip:''' Expand the "<u>Search summary</u>" section near the top by clicking it).		What are the sizes (in basepairs) of the databases we used for the two BLAST searches? ('''Tip:''' Expand the "<u>Search summary</u>" section near the top by clicking it).

	[[Image:Office-notes-line_drawing.png\|30px\|left]]		[[Image:Office-notes-line_drawing.png\|30px\|left]]
	:'''QUESTION 1.5''':		:'''QUESTION 1.6''':
	:*What is the ratio between the database sizes in the two BLAST searches?		:*What is the ratio between the database sizes in the two BLAST searches?
	:*What is the ratio between the E-values (for the best human hits) in the two BLAST searches?		:*What is the ratio between the E-values (for the best human hits) in the two BLAST searches?