ExGenbank-new-answers - Revision history

Carol at 12:13, 1 September 2026

2026-09-01T12:13:34Z

← Older revision		Revision as of 14:13, 1 September 2026
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	~~Note: numbers in Part 2 and Part 3 are updated on September 6, 2023.~~

	== Part 1 ==		== Part 1 ==

Carol: /* Part 2 */

2026-08-28T14:58:26Z

Part 2

← Older revision		Revision as of 16:58, 28 August 2026
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	:which gives 21 hits, representing 13 organisms and some synthetic constructs.		:which gives 21 hits, representing 13 organisms and some synthetic constructs.
	:''Note'': the use of double quotes ("") to add two-word "kill phrases".		:''Note'': the use of double quotes ("") to add two-word "kill phrases".
	:''~~Note~~'': '''don't kill "insulin precursor"!''' Insulin is always synthesized as a precursor, preproinsulin, that contains both a signal peptide, a propeptide, and the two mature chains. More about insulin in the exercises next week.		:''Note2'': '''don't kill "insulin precursor"!''' Insulin is always synthesized as a precursor, preproinsulin, that contains both a signal peptide, a propeptide, and the two mature chains. More about insulin in the exercises next week.
			:''Note3'': Notice the little amount of sequences of insulins genes we can find. There are genome species like dog and cat which are somewhat well studied but still do not appear here. Why is that? Most of the entries where Insulin is on the title, had been sequenced individually for that gene. Nowadays sequencing has become very cheap and it is easier to sequence entire genomes. If you do a search of insulin in NCBI gene, you will get hundreds of entries, however looking at the nucleotide sequences where they are stored is a bigger chunk of the genome. How to deal with that type of data is a matter of another lecture and another course such as the [https://teaching.healthtech.dtu.dk/22126/index.php/22126_-_Next_Generation_Sequencing_Analysis NGS course]

	== Part 3 ==		== Part 3 ==

Carol: /* Part 3 */

2026-08-28T14:49:49Z

Part 3

← Older revision		Revision as of 16:49, 28 August 2026
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	:It will never be possible to do this query perfectly - a good attempt could be:		:It will never be possible to do this query perfectly - a good attempt could be:
	"alcohol dehydrogenase"[title] complete[title] NOT mRNA[title] NOT synthetic[title]		"alcohol dehydrogenase"[title] complete[title] NOT mRNA[title] NOT synthetic[title]
	:which gives ~~2179~~ hits.		:which gives 2189 hits.
	:''Note'': as many as 360 of these hits are from one organism, Populus nigra (Poplar tree).		:''Note'': as many as 360 of these hits are from one organism, Populus nigra (Poplar tree).

Carol: /* Part 2 */

2026-08-28T14:41:26Z

Part 2

← Older revision		Revision as of 16:41, 28 August 2026
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	;QUESTION 2.4:		;QUESTION 2.4:
	:a) 9 hits.		:a) 9 hits.
	:b) 15 hits.		:b) 18 hits.
	:c) Accession codes: '''AH002844 J00265 J00268''', Locus name: '''AH002844''', Definition (title): "Human insulin gene, complete cds".		:c) Accession codes: '''AH002844 J00265 J00268''', Locus name: '''AH002844''', Definition (title): "Human insulin gene, complete cds".

Carol: /* Part 2 */

2026-08-28T14:39:51Z

Part 2

← Older revision		Revision as of 16:39, 28 August 2026
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	;QUESTION 2.3:		;QUESTION 2.3:
	:a) ~~5609~~ hits.		:a) 5616 hits.
	:b) Yes (except for 10 hits that are synthetic constructs, but based on human sequence). See the "Top Organisms" box on the right.		:b) Yes (except for 10 hits that are synthetic constructs, but based on human sequence). See the "Top Organisms" box on the right.
	:c) No.		:c) No.

Carol: /* Part 2 */

2026-08-28T14:34:30Z

Part 2

← Older revision		Revision as of 16:34, 28 August 2026
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	;QUESTION 2.2		;QUESTION 2.2
	:a) 20,493 hits.		:a) 20,493 hits.
	:b) Yes, it is ~~among the hits~~ on the ~~first page of results~~.		:b) Yes. There is a gene card, appearing in this search pointing to the insulin gene, as this is a very popular gene. The human insulin gene entry appears second on the list.
	::Title: '''Homo sapiens insulin (INS) gene, complete cds'''		::Title: '''Homo sapiens insulin (INS) gene, complete cds'''
	::Accession: '''AH002844'''		::Accession: '''AH002844'''

Carol: /* Part 2 */

2026-08-28T14:32:02Z

Part 2

← Older revision		Revision as of 16:32, 28 August 2026
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	;QUESTION 2.2		;QUESTION 2.2
	:a) 18,~~838~~ hits.		:a) 20,493 hits.
	:b) Yes, it is among the hits on the first page of results.		:b) Yes, it is among the hits on the first page of results.
	::Title: '''Homo sapiens insulin (INS) gene, complete cds'''		::Title: '''Homo sapiens insulin (INS) gene, complete cds'''

Carol: /* Part 2 */

2026-08-28T14:17:23Z

Part 2

← Older revision		Revision as of 16:17, 28 August 2026
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	;QUESTION 2.1:		;QUESTION 2.1:
	:a) ~~252~~,~~430~~ hits <!-- (you can see the "Sequence type" overview in the margin on the left). In total there are xxx,xxx hits (that includes xx,xxx [https://en.wikipedia.org/wiki/Expressed_sequence_tag EST] hits and xx [https://en.wikipedia.org/wiki/Genome_survey_sequence GSS] hits). -->		:a) 274,233 hits
	:b) No. There is ''e.g.'' the first hit, '''M57671.1''', "Octodon degus insulin mRNA, complete cds" which is from a [http://en.wikipedia.org/wiki/Degu Degu], a rat-like carnivore from Chile. In fact, you can see in the right side of the results page that only 11,521 hits are from human. There is no reason to expect only human results from GenBank, since it is not a human-centric database.		:b) No. There is ''e.g.'' the first hit, '''M57671.1''', "Octodon degus insulin mRNA, complete cds" which is from a [http://en.wikipedia.org/wiki/Degu Degu], a rat-like carnivore from Chile. In fact, you can see in the right side of the results page that only 11,521 hits are from human. There is no reason to expect only human results from GenBank, since it is not a human-centric database.
	:c) No. There are many hits to complete or partial chromosome sequences which contain a lot of other genes. An example is '''JWIN03000075.1''', "Camelus dromedarius breed African isolate Drom800 Contig74, whole genome shotgun sequence".		:c) No. There are many hits to complete or partial chromosome sequences which contain a lot of other genes. An example is '''JWIN03000075.1''', "Camelus dromedarius breed African isolate Drom800 Contig74, whole genome shotgun sequence".

Carol: /* Part 2 */

2026-08-28T14:00:21Z

Part 2

← Older revision		Revision as of 16:00, 28 August 2026
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	== Part 2 ==		== Part 2 ==

	;QUESTION 2.1.1:		;QUESTION 2.1:
	:a) 252,430 hits <!-- (you can see the "Sequence type" overview in the margin on the left). In total there are xxx,xxx hits (that includes xx,xxx [https://en.wikipedia.org/wiki/Expressed_sequence_tag EST] hits and xx [https://en.wikipedia.org/wiki/Genome_survey_sequence GSS] hits). -->		:a) 252,430 hits <!-- (you can see the "Sequence type" overview in the margin on the left). In total there are xxx,xxx hits (that includes xx,xxx [https://en.wikipedia.org/wiki/Expressed_sequence_tag EST] hits and xx [https://en.wikipedia.org/wiki/Genome_survey_sequence GSS] hits). -->
	:b) No. There is ''e.g.'' the first hit, '''M57671.1''', "Octodon degus insulin mRNA, complete cds" which is from a [http://en.wikipedia.org/wiki/Degu Degu], a rat-like carnivore from Chile. In fact, you can see in the right side of the results page that only 11,521 hits are from human. There is no reason to expect only human results from GenBank, since it is not a human-centric database.		:b) No. There is ''e.g.'' the first hit, '''M57671.1''', "Octodon degus insulin mRNA, complete cds" which is from a [http://en.wikipedia.org/wiki/Degu Degu], a rat-like carnivore from Chile. In fact, you can see in the right side of the results page that only 11,521 hits are from human. There is no reason to expect only human results from GenBank, since it is not a human-centric database.
	:c) No. There are many hits to complete or partial chromosome sequences which contain a lot of other genes. An example is '''JWIN03000075.1''', "Camelus dromedarius breed African isolate Drom800 Contig74, whole genome shotgun sequence".		:c) No. There are many hits to complete or partial chromosome sequences which contain a lot of other genes. An example is '''JWIN03000075.1''', "Camelus dromedarius breed African isolate Drom800 Contig74, whole genome shotgun sequence".
			:d) In the <u>Search details</u> box, you find "<tt>insulin[All Fields]</tt>".

	;QUESTION 2.1.2:		;QUESTION 2.2
	~~:a) In the <u>Search details</u> box, you find "<tt>insulin[All Fields]</tt>".~~

	~~;QUESTION 2.1.3~~
	:a) 18,838 hits.		:a) 18,838 hits.
	:b) Yes, it is among the hits on the first page of results.		:b) Yes, it is among the hits on the first page of results.
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	:c) <tt>("Homo sapiens"[Organism] OR human[All Fields]) AND insulin[All Fields]</tt>		:c) <tt>("Homo sapiens"[Organism] OR human[All Fields]) AND insulin[All Fields]</tt>

	;QUESTION 2.2:		;QUESTION 2.3:
	:a) 5609 hits.		:a) 5609 hits.
	:b) Yes (except for 10 hits that are synthetic constructs, but based on human sequence). See the "Top Organisms" box on the right.		:b) Yes (except for 10 hits that are synthetic constructs, but based on human sequence). See the "Top Organisms" box on the right.
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	:* Many entries are mRNA and therefore not gene entries.		:* Many entries are mRNA and therefore not gene entries.

	;QUESTION 2.3:		;QUESTION 2.4:
	:a) 9 hits.		:a) 9 hits.
	:b) 15 hits.		:b) 15 hits.
	:c) Accession codes: '''AH002844 J00265 J00268''', Locus name: '''AH002844''', Definition (title): "Human insulin gene, complete cds".		:c) Accession codes: '''AH002844 J00265 J00268''', Locus name: '''AH002844''', Definition (title): "Human insulin gene, complete cds".

	;QUESTION 2.4:		;QUESTION 2.5:
	:The important thing here is not the precise search string, but that you understand the principle of using "kill-words". One possible answer could be:		:The important thing here is not the precise search string, but that you understand the principle of using "kill-words". One possible answer could be:
	::insulin[title] complete[title] NOT mRNA[title] NOT receptor[title] NOT receptor-like[title] NOT "insulin like"[title] NOT "insulin degrading"[title] NOT "growth factor"[title] NOT "family member"[title] NOT "insulin induced"[title] NOT "insulin dependent"[title] NOT "insulin promoter"[title]		::insulin[title] complete[title] NOT mRNA[title] NOT receptor[title] NOT receptor-like[title] NOT "insulin like"[title] NOT "insulin degrading"[title] NOT "growth factor"[title] NOT "family member"[title] NOT "insulin induced"[title] NOT "insulin dependent"[title] NOT "insulin promoter"[title]

Carol: /* Part 1 */

2026-08-28T13:32:02Z

Part 1

← Older revision		Revision as of 15:32, 28 August 2026
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	;QUESTION 1.3:		;QUESTION 1.3:
	:The downloaded file has Unix line endings. Remember from [[Plain text files and Geany]] that line endings are indicated in the status line at the bottom of the Geany window.<!-- by the letters "U", "W" or "M" in the lower right hand corner of the jEdit window. --> <!-- ''This means that you would have had trouble opening it in Notepad on Windows.'' -->

	~~;QUESTION 1.4:~~
	:a) The "join" statements defines how to extract the coding sequence from the entire length of DNA in the entry: "<tt>join(1104..1192,1306..1510,1614..1742)</tt>" is basically a recipe stating to paste together the three intervals - and we'll get the ''protein coding'' part of the gene: the coding exons glued together. The CDS will always start with a START codon (''e.g.'' <tt>ATG</tt>) and end with a STOP codon (''e.g.'' <tt>TAA</tt>).		:a) The "join" statements defines how to extract the coding sequence from the entire length of DNA in the entry: "<tt>join(1104..1192,1306..1510,1614..1742)</tt>" is basically a recipe stating to paste together the three intervals - and we'll get the ''protein coding'' part of the gene: the coding exons glued together. The CDS will always start with a START codon (''e.g.'' <tt>ATG</tt>) and end with a STOP codon (''e.g.'' <tt>TAA</tt>).
	:b) The gene contains three coding exons. ''Note'': from a CDS definition we don't get any information about ''UnTranslated Regions'' (UTR's) that are often found before and after the coding region in the mRNA).		:b) The gene contains three coding exons. ''Note'': from a CDS definition we don't get any information about ''UnTranslated Regions'' (UTR's) that are often found before and after the coding region in the mRNA).

	;QUESTION 1.5:		;QUESTION 1.4:
	:The first number is the Gene Identifier (taken from the VERSION line in the header). The subsequent numbers are the positions (coordinates) in the original gene entry (taken from the <tt>join</tt> line).		:The first number is the Gene Identifier (taken from the VERSION line in the header). The subsequent numbers are the positions (coordinates) in the original gene entry (taken from the <tt>join</tt> line).