ExPSIBLAST answer - Revision history

Henni: /* Finding a remote homolog (on your own) */

2025-11-10T10:15:53Z

Finding a remote homolog (on your own)

← Older revision		Revision as of 12:15, 10 November 2025
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	* '''QUESTION 14''': How many significant (E<0.005) hits do you find now? What is the E-value of the best hit?		* '''QUESTION 14''': How many significant (E<0.005) hits do you find now? What is the E-value of the best hit?
	Answer: There are 2 significant hits:		Answer: There are 2 significant hits:
	* "GPI transamidase component Gaa1" from ''Trypanosoma melophagium'' with an E-value of 1e-05		* "GPI transamidase component Gaa1" from ''Trypanosoma melophagium'' with an E-value of 4e-05
	* "putative GPI transamidase component GAA1" from ''Trypanosoma theileri'' withs an E-value of 8e-04		* "putative GPI transamidase component GAA1" from ''Trypanosoma theileri'' withs an E-value of 3e-03

Henni: /* Saving and reusing the PSSM */

2025-11-10T09:08:52Z

Saving and reusing the PSSM

← Older revision		Revision as of 11:08, 10 November 2025
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	* '''QUESTION 9''': What are the PDB identifiers and the E-values for the two best PDB hits?		* '''QUESTION 9''': What are the PDB identifiers and the E-values for the two best PDB hits?
	Answer: 5HXY_A with an E-value of 8´2×10<sup>-19</sup>; 4A8E_A with an E-value of 2×10<sup>-17</sup>~~, ,~~		Answer: 5HXY_A with an E-value of 8´2×10<sup>-19</sup>; 4A8E_A with an E-value of 2×10<sup>-17</sup>.

	* '''QUESTION 10''': What are the values for Query coverage, sequence identity, and sequence similarity (Positives) for the two best PDB hits?		* '''QUESTION 10''': What are the values for Query coverage, sequence identity, and sequence similarity (Positives) for the two best PDB hits?

Henni: /* One more round */

2025-11-10T09:08:08Z

One more round

@@ Line 51: / Line 51: @@
 === One more round ===
 * '''QUESTION 12''': Answer questions 8-10 again for the new search.
-'''Answer:''' There are now 17 significant hits. The two best are still 4A8E_A and 5HXY_A.
+'''Answer:''' There are now 18 significant hits. The two best are still 4A8E_A and 5HXY_A.
   ID      E      cov   ident  sim/pos
-HXY_A  5e-34  63%   18%    32%
+A8E_A  3e-55  65%   18%    36%
-A8E_A  1e-30  65%   17%    33%
+HXY_A  3e-41  61%   18%    32%
 == Finding a remote homolog (on your own) ==

Henni: /* Saving and reusing the PSSM */

2025-11-10T08:50:13Z

Saving and reusing the PSSM

@@ Line 34: / Line 34: @@
 * '''QUESTION 9''': What are the PDB identifiers and the E-values for the two best PDB hits?
-Answer: 4A8E_A with an E-value of 2&times;10<sup>-19</sup>, 5HXY_A with an E-value of 8&times;10<sup>-19</sup>,
+Answer: 5HXY_A with an E-value of 8´2&times;10<sup>-19</sup>; 4A8E_A with an E-value of 2&times;10<sup>-17</sup>, ,
 * '''QUESTION 10''': What are the values for Query coverage, sequence identity, and sequence similarity (Positives) for the two best PDB hits?
@@ Line 40: / Line 40: @@
 '''Answer:'''
   ID      cov   ident  sim/pos
-A8E_A  46%   21%    39%
+HXY_A  46%   20%    35%
-HXY_A  61%   18%    31%
+A8E_A  63%   18%    37%

Henni: /* Saving and reusing the PSSM */

2025-11-09T14:20:21Z

Saving and reusing the PSSM

← Older revision		Revision as of 16:20, 9 November 2025
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	=== Saving and reusing the PSSM ===		=== Saving and reusing the PSSM ===
	* '''QUESTION 8''': Do you find any significant PDB hits now? If yes, how many?		* '''QUESTION 8''': Do you find any significant PDB hits now? If yes, how many?
	Answer: Yes, 13		Answer: Yes, 16

	* '''QUESTION 9''': What are the PDB identifiers and the E-values for the two best PDB hits?		* '''QUESTION 9''': What are the PDB identifiers and the E-values for the two best PDB hits?

Henni: /* Constructing the PSSM */

2025-11-09T13:33:10Z

Constructing the PSSM

← Older revision		Revision as of 15:33, 9 November 2025
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	Answer: Hit #500 has an E-value of 8e-14, i.e., much much smaller than 0.005.		Answer: Hit #500 has an E-value of 8e-14, i.e., much much smaller than 0.005.

	* '''QUESTION 6''': How large a fraction of the query sequence do the 20 most significant hits match (do not include the ~~first hit since this is identical to~~ the ~~query~~)?		* '''QUESTION 6''': How large a fraction of the query sequence do the 20 most significant hits match (do not include the the 100% identity match))?
	Answer: 53%-87%		Answer: 53%-87%

	* '''QUESTION 7''': Why does BLAST come up with more significant hits in the second iteration? Make sure you answer this question and understand what is going on!		* '''QUESTION 7''': Why does BLAST come up with more significant hits in the second iteration? Make sure you answer this question and understand what is going on!
	Answer: During the first iteration a generic ~~Blosum62~~ substitution matrix was used, and hits found there were made into a multiple alignment and next a more sensitive position-specific-substitution-matrix (PSSM). This is why more sequences are found in the second iteration. A PSSM can capture evolutionary sequence information i.e. conserved regions, active sites and regions with less evolutionary pressure (many different amino acids at a certain position).		Answer: During the first iteration a generic BLOSUM62 substitution matrix was used, and hits found there were made into a multiple alignment and next a more sensitive position-specific-substitution-matrix (PSSM). This is why more sequences are found in the second iteration. A PSSM can capture evolutionary sequence information i.e. conserved regions, active sites and regions with less evolutionary pressure (many different amino acids at a certain position).

	=== Saving and reusing the PSSM ===		=== Saving and reusing the PSSM ===

Henni: /* Trying another approach */

2025-11-08T16:29:22Z

Trying another approach

← Older revision		Revision as of 18:29, 8 November 2025
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	Answer: For most hits between 45 and 55%. A few hits are lower, down to 5%.		Answer: For most hits between 45 and 55%. A few hits are lower, down to 5%.

	* '''QUESTION 4''': (deleted) ~~<!--~~ Do you find any PDB hits among the significant hits?		<!--* '''QUESTION 4''': (deleted) Do you find any PDB hits among the significant hits?
	Answer: No, of course not. If there were any significant PDB hits, we would have found them under QUESTION 1.-->		Answer: No, of course not. If there were any significant PDB hits, we would have found them under QUESTION 1.-->

	=== Constructing the PSSM ===		=== Constructing the PSSM ===
	* '''QUESTION 5''': How many significant hits does BLAST find (E-value < 0.005)?		* '''QUESTION 4''': How many significant hits does BLAST find (E-value < 0.005)?
	Answer: 500 (actually, much more than 500 hits, but BLAST by default only shows 500 ~~— note that~~ the ~~last~~ hit has an E-value much much smaller than 0.005)		Answer: 500 (actually, much more than 500 hits, but BLAST by default only shows 500)

			* '''QUESTION 5''': What is the E-value of the ''least'' significant hit shown on the results page?
			Answer: Hit #500 has an E-value of 8e-14, i.e., much much smaller than 0.005.

	* '''QUESTION 6''': How large a fraction of the query sequence do the 20 most significant hits match (do not include the first hit since this is identical to the query)?		* '''QUESTION 6''': How large a fraction of the query sequence do the 20 most significant hits match (do not include the first hit since this is identical to the query)?
	Answer: ~~approx. 50~~-~~60% sequence coverage, except one (#2) that is 84~~%.		Answer: 53%-87%

	* '''QUESTION 7''': Why does BLAST come up with more significant hits in the second iteration? Make sure you answer this question and understand what is going on!		* '''QUESTION 7''': Why does BLAST come up with more significant hits in the second iteration? Make sure you answer this question and understand what is going on!

Henni: /* Trying another approach */

2025-11-08T16:03:05Z

Trying another approach

← Older revision		Revision as of 18:03, 8 November 2025
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	Answer: After the first iteration, 181 significant hits are found.		Answer: After the first iteration, 181 significant hits are found.

	* '''QUESTION 3''': How large a fraction of the query sequence do the significant hits match (excluding the ~~identical~~ match)?		* '''QUESTION 3''': How large a fraction of the query sequence do the significant hits typically match (excluding the 100% identity match)?
	Answer: For most hits between 45 and 55~~%. One hit (#2) is 84~~%. A few hits are lower, down to 11%.		Answer: For most hits between 45 and 55%. A few hits are lower, down to 5%.

	* '''QUESTION 4''': (deleted) <!-- Do you find any PDB hits among the significant hits?		* '''QUESTION 4''': (deleted) <!-- Do you find any PDB hits among the significant hits?

Henni: /* Trying another approach */

2025-11-08T15:52:12Z

Trying another approach

← Older revision		Revision as of 17:52, 8 November 2025
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	==Trying another approach==		==Trying another approach==
	* '''QUESTION 2''': How many significant hits does BLAST find (E-value < 0.005)?		* '''QUESTION 2''': How many significant hits does BLAST find (E-value < 0.005)?
	Answer: After the first iteration, ~~494~~ hits are found.		Answer: After the first iteration, 181 significant hits are found.

	* '''QUESTION 3''': How large a fraction of the query sequence do the significant hits match (excluding the identical match)?		* '''QUESTION 3''': How large a fraction of the query sequence do the significant hits match (excluding the identical match)?
	Answer: For most hits between 45 and 55%. One hit (#2) is 84%. A few hits are lower, down to 11%.		Answer: For most hits between 45 and 55%. One hit (#2) is 84%. A few hits are lower, down to 11%.

	* '''QUESTION 4''': Do you find any PDB hits among the significant hits?		* '''QUESTION 4''': (deleted) <!-- Do you find any PDB hits among the significant hits?
	Answer: No, of course not. If there were any significant PDB hits, we would have found them under QUESTION 1.		Answer: No, of course not. If there were any significant PDB hits, we would have found them under QUESTION 1.-->

	=== Constructing the PSSM ===		=== Constructing the PSSM ===

Henni at 15:33, 8 November 2025

2025-11-08T15:33:32Z

← Older revision		Revision as of 17:33, 8 November 2025
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	Note: E-values etc. are found November 8, ~~2023~~.		Note: E-values etc. are found November 8, 2025.

	== When BLAST fails ==		== When BLAST fails ==