ExBlast-Answers3 - Revision history

Carol: /* QUESTION 1.4 */

2025-10-03T09:43:56Z

QUESTION 1.4

← Older revision		Revision as of 11:43, 3 October 2025
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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): ~~289~~,~~748~~,~~744~~,~~057~~ letters (= basepairs), Human G+T: 4,~~013~~,~~923~~,~~595~~ letters (= basepairs).		nt(Human): 2,933,612,979,911 letters (= basepairs), Human G+T: 4,017,001,775 letters (= basepairs).

	===QUESTION 1.5===		===QUESTION 1.5===

Carol: /* QUESTION 1.2 */

2025-10-03T09:41:52Z

QUESTION 1.2

← Older revision		Revision as of 11:41, 3 October 2025
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	:identity: 74.49% and query coverage: 76%		:identity: 74.49% and query coverage: 76%
	* ''what is the E-value?''		* ''what is the E-value?''
	:2e-48 (meaning 2×10<sup>-48</sup>)		:2e-47 (meaning 2×10<sup>-48</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.		:Yes, there are five gaps in the query sequence and two gaps in the database sequence, totaling 15 positions.

Carol: /* QUESTION 1.5 */

2025-10-03T09:41:21Z

QUESTION 1.5

← Older revision		Revision as of 11:41, 3 October 2025
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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?''
	:~~289748744057~~ / ~~4013923595~~ = <u>72</u>		: 2,933,612,979,911 / 4,017,001,775 = <u>730</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-48 / 3e-50 = <u>66</u>		:2e-47 / 3e-50 = <u>666</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-48 / 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.
	*''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.

Carol: /* QUESTION 1.2 */

2025-10-03T09:33:41Z

QUESTION 1.2

← Older revision		Revision as of 11:33, 3 October 2025
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	===QUESTION 1.2===		===QUESTION 1.2===
	* ''what is the identifier (Accession)?''		* ''what is the identifier (Accession)?''
	:MT335691.1 or MT335690.1 or MT335689.1 ~~(or a handful more)~~, 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
	* ''what is the alignment score ("max score")?''		* ''what is the alignment score ("max score")?''
	:205		:205

Carol at 09:33, 3 October 2025

2025-10-03T09:33:18Z

← Older revision		Revision as of 11:33, 3 October 2025
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	===QUESTION 1.2===		===QUESTION 1.2===
	* ''what is the identifier (Accession)?''		* ''what is the identifier (Accession)?''
	:MT335690.1 or MT335689.1 (or a handful more), they have the same score and are therefore equally good		:MT335691.1 or MT335690.1 or MT335689.1 (or a handful more), they have the same score and are therefore equally good
	* ''what is the alignment score ("max score")?''		* ''what is the alignment score ("max score")?''
	:205		:205
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	:identity: 74.49% and query coverage: 76%		:identity: 74.49% and query coverage: 76%
	* ''what is the E-value?''		* ''what is the E-value?''
	:7e-48 (meaning 2×10<sup>-48</sup>)		:2e-48 (meaning 2×10<sup>-48</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.		:Yes, there are five gaps in the query sequence and two gaps in the database sequence, totaling 15 positions.

Carol: /* QUESTION 1.2 */

2025-10-03T09:21:27Z

QUESTION 1.2

← Older revision		Revision as of 11:21, 3 October 2025
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	===QUESTION 1.2===		===QUESTION 1.2===
	* ''what is the identifier (Accession)?''		* ''what is the identifier (Accession)?''
	:~~NM_001185098~~ or ~~NM_001185097~~ (or a handful more), they have the same score and are therefore equally good		:MT335690.1 or MT335689.1 (or a handful more), they have the same score and are therefore equally good
	* ''what is the alignment score ("max score")?''		* ''what is the alignment score ("max score")?''
	:205		:205

Carol: /* QUESTION 1.2 */

2025-10-03T09:20:56Z

QUESTION 1.2

← Older revision		Revision as of 11:20, 3 October 2025
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	:identity: 74.49% and query coverage: 76%		:identity: 74.49% and query coverage: 76%
	* ''what is the E-value?''		* ''what is the E-value?''
	:2e-48 (meaning 2×10<sup>-48</sup>)		:7e-48 (meaning 2×10<sup>-48</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.		:Yes, there are five gaps in the query sequence and two gaps in the database sequence, totaling 15 positions.

Henni: /* QUESTION 3.1 */

2024-11-15T15:14:33Z

QUESTION 3.1

← Older revision		Revision as of 17:14, 15 November 2024
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	'''STEP 1 - cleaning up the sequence: '''		'''STEP 1 - cleaning up the sequence: '''

	*''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.''

	>CLONE12		>CLONE12

Carol at 06:13, 1 October 2024

2024-10-01T06:13:47Z

← Older revision		Revision as of 08:13, 1 October 2024
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	: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.		: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.		: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===		===QUESTION 3.1===
	'''STEP 1 - cleaning up the sequence: '''		'''STEP 1 - cleaning up the sequence: '''

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

2024-10-01T03:22:30Z

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

← Older revision		Revision as of 05:22, 1 October 2024
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	==Part 3: using BLAST to transfer functional information by finding homologs==		==Part 3: using BLAST to transfer functional information by finding homologs==

	===QUESTION 3.1===		<!-- ===QUESTION 3.1===

	*''Do we get any significant hits?''		*''Do we get any significant hits?''
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	: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.		: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.		: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 3.3===		===QUESTION 3.1===
	'''STEP 1 - cleaning up the sequence: '''		'''STEP 1 - cleaning up the sequence: '''