ExBlast-Answers new - Revision history

Carol: /* QUESTION 2.3 */

2026-09-22T08:48:16Z

QUESTION 2.3

← Older revision		Revision as of 10:48, 22 September 2026
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	: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).		: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...		Generating Random Sequence 1 for BLAST...
	DTGVHDAQEIGITCQFQPVCFLFSP		DTGVHDAQEIGITCQFQPVCFLFSP
	**Alignment** 1		**Alignment** 1
	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]		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_243336483		Accession: WP_243336483
	Length: 827		Length: 827
	Max Score: 69.0		Max Score: 69.0
	Bits: 31.187		Bits: 31.187
	Identities: 13		Identities: 13
	Align_length: 23		Align_length: 23
	Gaps: 0		Gaps: 0
	%Ident: 56.52 %		%Ident: 56.52 %
	Query Cover: 92 %		Query Cover: 92 %
	E value: 1.12e+02		E value: 1.12e+02
	Query: TGVHDAQEIGITCQFQPVCFLFS		Query: TGVHDAQEIGITCQFQPVCFLFS
	Match: T VHDA I +T QF P C LF+		Match: T VHDA I +T QF P C LF+
	Subject: TAVHDALLIDLTSQFHPACGLFT		Subject: TAVHDALLIDLTSQFHPACGLFT

Carol: /* QUESTION 2.3 */

2026-09-22T08:47:40Z

QUESTION 2.3

← Older revision		Revision as of 10:47, 22 September 2026
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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).

	**Alignment** 1		Generating Random Sequence 1 for BLAST...
	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~~]		DTGVHDAQEIGITCQFQPVCFLFSP
	Accession: ~~WP_179589105~~		**Alignment** 1
	Length: ~~1782~~		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]
	Max Score: 67.0		Accession: WP_243336483
	Bits: 30.~~4166~~		Length: 827
	Identities: 8		Max Score: 69.0
	Align_length: 22		Bits: 31.187
	Gaps: 0		Identities: 13
	%Ident: 36.36 %		Align_length: 23
	Query Cover: 88 %		Gaps: 0
	E value: 1.~~25e~~+02		%Ident: 56.52 %
	~~LTNNVNMHWTLPYTVSHVYVNP~~		Query Cover: 92 %
	~~L ++ HW~~ +P+~~T+SH++ +P~~		E value: 1.12e+02
	~~LAARISQHWCVPFTISHIFDHP~~		Query: TGVHDAQEIGITCQFQPVCFLFS
			Match: T VHDA I +T QF P C LF+
			Subject: TAVHDALLIDLTSQFHPACGLFT

Carol: /* QUESTION 2.1 */

2026-09-21T16:36:27Z

QUESTION 2.1

← Older revision		Revision as of 18:36, 21 September 2026
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	:1-15		: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===

Carol: /* QUESTION 2.1 */

2026-09-21T16:33:07Z

QUESTION 2.1

← Older revision		Revision as of 18:33, 21 September 2026
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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?'':

Carol: /* QUESTION 2.1 */

2026-09-21T16:23:59Z

QUESTION 2.1

← Older revision		Revision as of 18:23, 21 September 2026
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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?'':
Line 101:		Line 99:

	*''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''': we chose to use an E-value threshold of 50.0. The default is 0.05.

Carol: /* QUESTION 1.6 */

2026-09-21T14:01:00Z

QUESTION 1.6

← Older revision		Revision as of 16:01, 21 September 2026
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	*''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?''
	: 1,081,933,534,067 / 4,017,001,775 = <u>~~~270~~</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? ''
	:7e-168 / 3e-170 = <u>~~270~~</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.

Carol: /* QUESTION 1.6 */

2026-09-21T13:58:17Z

QUESTION 1.6

← Older revision		Revision as of 15:58, 21 September 2026
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	*''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>~270</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>270</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 "2e-47 / 3e-50" directly and the answer will show up in the results.

Carol: /* QUESTION 1.5 */

2026-09-21T13:55:25Z

QUESTION 1.5

← Older revision		Revision as of 15:55, 21 September 2026
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	''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 1.6===		===QUESTION 1.6===

Carol: /* Part 1: Your first BLAST search */

2026-09-21T13:52:25Z

Part 1: Your first BLAST search

← Older revision		Revision as of 15:52, 21 September 2026
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	:The max score is 708 bits		: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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	===QUESTION 1.3===		===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): 2,933,612,979,911 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?''

Carol: /* Part 1: Your first BLAST search */

2026-09-21T13:47:46Z

Part 1: Your first BLAST search

← Older revision		Revision as of 15:47, 21 September 2026
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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%
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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===
	* ''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		:MT335691.1 or MT335690.1 or MT335689.1, they have the same score and are therefore equally good