ExPairwiseAlignment-AnswersEng - Revision history

Henni at 13:57, 22 September 2026

2026-09-22T13:57:57Z

← Older revision		Revision as of 14:57, 22 September 2026
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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==

Henni: /* Q9 */

2026-09-10T15:09:15Z

← Older revision		Revision as of 16:09, 10 September 2026
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	It is clear from the local alignment and from the global alignment ''without'' end gap penalties that the prokaryotic protease matches only a single area in the middle of the human protease. In contrast, this is not clear in the global alignment ''with'' end gap penalties, which "spreads" the short sequence over the entire length.		It is clear from the local alignment and from the global alignment ''without'' end gap penalties that the prokaryotic protease matches only a single area in the middle of the human protease. In contrast, this is not clear in the global alignment ''with'' end gap penalties, which "spreads" the short sequence over the entire length.

	Note that the global alignment ''without'' end ~~gaps~~ can be regarded as a kind of compromise between global and local alignment.		Note that the global alignment ''without'' end gap penalties can be regarded as a kind of compromise between global and local alignment.

	For distantly related sequences, it would be best to use local alignment; this would actually provide an optimal analysis of the comparable part of the sequences.		For distantly related sequences, it would be best to use local alignment; this would actually provide an optimal analysis of the comparable part of the sequences.

Henni: /* Q9 */

2026-09-10T15:08:38Z

← Older revision		Revision as of 16:08, 10 September 2026
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	===Q9===		===Q9===

	It is clear from the local alignment and from ~~theglobal~~ alignment ''without'' end ~~gaps~~ that the prokaryotic protease matches only a single area in the middle of the human protease. In contrast, this is not clear in the global alignment ''with'' end ~~gaps~~, which "spreads" the short sequence over the entire length.		It is clear from the local alignment and from the global alignment ''without'' end gap penalties that the prokaryotic protease matches only a single area in the middle of the human protease. In contrast, this is not clear in the global alignment ''with'' end gap penalties, which "spreads" the short sequence over the entire length.

	Note that the global alignment ''without'' end gaps can be regarded as a kind of compromise between global and local alignment.		Note that the global alignment ''without'' end gaps can be regarded as a kind of compromise between global and local alignment.

Henni: /* Q7 */

2026-09-10T15:06:09Z

← Older revision		Revision as of 16:06, 10 September 2026
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	# Score: 158.5		# Score: 158.5

	(Alignment not shown)		(Alignment not shown. But this time, it looks completely different from the one made with end gap penalties.)

	===Q8===		===Q8===

Henni: /* Q13 */

2026-09-10T15:04:15Z

Q13

← Older revision		Revision as of 16:04, 10 September 2026
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	===Q13===		===Q13===

	# Length: ~~1255~~		# Length: 1252
	# Identity: 192/~~1255~~ (15.3%)		# Identity: 192/1252 (15.3%)
	# Similarity: 228/~~1255~~ (18.2%)		# Similarity: 228/1252 (18.2%)
	# Gaps: ~~1011~~/~~1255~~ (80.6%)		# Gaps: 1006/1252 (80.4%)
	# Score: 895,576		# Score: 895,576

	Note how the sequences are stretched out each time the amino acids are not similar.		Note how the sequences are stretched out each time the amino acids are not similar.

	This alignment does not provide any ~~obvious~~ biological insight. If the gap penalty is low enough, ''any'' alignment gives a high score.		This alignment does not provide any biological insight. If the gap penalty is low enough, ''any'' alignment gives a high score.

	==Epilogue==		==Epilogue==

Henni: /* Q8 */

2026-09-10T14:58:55Z

← Older revision		Revision as of 15:58, 10 September 2026
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	# Gaps: 73/296 (24.7%)		# Gaps: 73/296 (24.7%)
	# Score: 173.0		# Score: 173.0
			<pre>
			Seq1 23 GSGVKVAVLDTGISTHPDLNIRGGASFVPGEPSTQDGNGHGTHVAGTIAA-------LNN 75
	~~SUBS_BACLE 23~~ GSGVKVAVLDTGISTHPDLNIRGGASFVPGEPSTQDGNGHGTHVAGTIAA 72		\|\|.....:\|:..::.:.\|.\|: .\|.\| ..\|..\|\|\|\|\|\| :\|\|\| ..\|
	\|\|.....:\|:..::.:.\|.\|: .\|.\| ..\|..\|\|\|\|\|\| :\|\|\|		Seq2 234 GSFGTAEMLNYSVNIYDDGNL---LSIV------TSGGAHGTHVA-SIAAGHFPEEPERN 283
	~~TPP2_HUMAN 234~~ GSFGTAEMLNYSVNIYDDGNL---LSIV------TSGGAHGTHVA-~~SIAA 273~~
			Seq1 76 SIGVLGVAPSAELYAVKV------LGASGSGSVSSIAQGLEWAGNNGMHVANLSLGSPS- 128
	~~SUBS_BACLE 73 LNNSIGVL~~-------~~GVAPSAELYAVKV------LGASGSGSVSSIAQGL 109~~		\|\|\|\|.\|::.::\|: ...:\|:\|.:.::.:.: \|:...:.\|.\|.\|..:
	~~\|..~~ \|\|\|\|.\|::.::\|: ...:\|:\|.:.::.:.:		Seq2 284 -----GVAPGAQILSIKIGDTRLSTMETGTGLIRAMIEVI----NHKCDLVNYSYGEATH 334
	~~TPP2_HUMAN 274 -----GHFPEEPERNGVAPGAQILSIKIGDTRLSTMETGTGLIRAMIEVI 318~~
			Seq1 129 --PSATLEQAVNSAT-SRGVLVVAASGNSG--AGSISYP-ARYANAMAVGATDQNN---- 178
	~~SUBS_BACLE 110 EWAGNNGMHVANLSLGSPS---PSATLEQAVNSAT-SRGVLVVAASGNSG~~ ~~155~~		.\|..:.:.:\|.\|. ...::.\|:::\|\|:\| ..::..\| ...::.:.\|\|\|....:
	\|:...:.\|.\|.\|..: .\|..:.:.:\|.\|. ...::.\|:::\|\|:\|		Seq2 335 WPNSGRICEVINEAVWKHNIIYVSSAGNNGPCLSTVGCPGGTTSSVIGVGAYVSPDMMVA 394
	~~TPP2_HUMAN 319 ----NHKCDLVNYSYGEATHWPNSGRICEVINEAVWKHNIIYVSSAGNNG 364~~
			Seq1 179 ----------NRASFSQYGAGLDIVAPGVNVQSTYPGSTYAS-----------LNGTSMA 217
	~~SUBS_BACLE 156 --AGSISYP-ARYANAMAVGATDQNN--------------NRASFSQYGA 188~~		\|:.::\|..\|...\| .\|.\|\|::.: \|\|...\|\| :\|\|\|\|\|:
	..::..\| ...::.:.\|\|\|....: ~~\|:.::\|..\|.~~		Seq2 395 EYSLREKLPANQYTWSSRGPSAD-GALGVSISA--PGGAIASVPNWTLRGTQLMNGTSMS 451
	~~TPP2_HUMAN 365 PCLSTVGCPGGTTSSVIGVGAYVSPDMMVAEYSLREKLPANQYTWSSRGP 414~~
			Seq1 218 TPHVAGAAALV----KQKNPSWSNVQIRNHLKNTATSLGSTNLY--GSGLVNAEAA 267
	~~SUBS_BACLE 189 GLDIVAPGVNVQSTYPGSTYAS~~-----------~~LNGTSMATPHVAGAAAL 227~~		:\|:..\|..\|\|: \|..\|..::...:\|..\|:\|\|\|....:..:: \|.\|::..:.\|
	..\| .\|.\|\|::.: \|\|...\|\| :\|\|\|\|\|:~~:\|:..\|..\|\|~~		Seq2 452 SPNACGGIALILSGLKANNIDYTVHSVRRALENTAVKADNIEVFAQGHGIIQVDKA 507
	~~TPP2_HUMAN 415 SAD~~-GALGVSISA--~~PGGAIASVPNWTLRGTQLMNGTSMSSPNACGGIAL 461~~		</pre>

	~~SUBS_BACLE 228 V~~----KQKNPSWSNVQIRNHLKNTATSLGSTNLY--GSGLVNAEAA 267
	: \|..\|..::...:\|..\|:\|\|\|....:..:: \|.\|::..:.\|
	~~TPP2_HUMAN 462 ILSGLKANNIDYTVHSVRRALENTAVKADNIEVFAQGHGIIQVDKA~~ 507

	===Q9===		===Q9===

Henni: /* Q3 */

2026-09-10T14:53:28Z

← Older revision		Revision as of 15:53, 10 September 2026
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	===Q3===		===Q3===
			'''Alignment Score: 916.00'''

	'''Length:''' 269, '''Identities:''' 176/269 (65.4%), '''Similarities:''' 214/269 (79.6%), '''Gaps:''' 0/269 (0.0%)		'''Length:''' 269, '''Identities:''' 176/269 (65.4%), '''Similarities:''' 214/269 (79.6%), '''Gaps:''' 0/269 (0.0%)

	~~# Length: 269~~		<pre>
	~~# Identity: 176/269 (65.4%)~~		Seq1 1 AQSVPWGISRVQAPAAHNRGLTGSGVKVAVLDTGISTHPDLNIRGGASFVPGEPSTQDGN 60
	~~# Similarity: 214/269 (79.6%)~~		:\|:\|\|\|\|\|\|.:....\|\|\|\|\|:.\|:\|.:\|\|\|\|\|\|\|\|::\|\|\|\|.\|.\|\|\|\|\|:..\|\|\|..\|.\|
	~~# Gaps: 0/269 (0.0%)~~		Seq2 93 SQTVPWGISFINTQQAHNRGIFGNGARVAVLDTGIASHPDLRIAGGASFISSEPSYHDNN 152
	~~# Score: 916.0~~
			Seq1 61 GHGTHVAGTIAALNNSIGVLGVAPSAELYAVKVLGASGSGSVSSIAQGLEWAGNNGMHVA 120
	~~SUBS_BACLE 1 AQSVPWGISRVQAPAAHNRGLTGSGVKVAVLDTGISTHPDLNIRGGASFV 50~~		\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|:\|\|\|\|\|\|\|..:\|\|\|\|::\|:\|\|\|:\|\|\|.\|\|.\|\|:.
	:\|:\|\|\|\|\|\|.:....\|\|\|\|\|:.\|:\|.:\|\|\|\|\|\|\|\|::\|\|\|\|.\|.\|\|\|\|\|:		Seq2 153 GHGTHVAGTIAALNNSIGVLGVAPSADLYAVKVLDRNGSGSLASVAQGIEWAINNNMHII 212
	~~ELYA_BACHD 93 SQTVPWGISFINTQQAHNRGIFGNGARVAVLDTGIASHPDLRIAGGASFI 142~~
			Seq1 121 NLSLGSPSPSATLEQAVNSATSRGVLVVAASGNSGAGSISYPARYANAMAVGATDQNNNR 180
	~~SUBS_BACLE 51 PGEPSTQDGNGHGTHVAGTIAALNNSIGVLGVAPSAELYAVKVLGASGSG 100~~		\|:\|\|\|\|.\|.\|:\|\|\|.\|\|\|.\|.:.\|:\|:\|.\|:\|\|:\|...::\|\|\|\|\|:..\|\|\|.\|.\|\|\|..\|
	..\|\|\|..\|.\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|:\|\|\|\|\|\|\|..:\|\|\|		Seq2 213 NMSLGSTSGSSTLELAVNRANNAGILLVGAAGNTGRQGVNYPARYSGVMAVAAVDQNGQR 272
	~~ELYA_BACHD 143 SSEPSYHDNNGHGTHVAGTIAALNNSIGVLGVAPSADLYAVKVLDRNGSG 192~~
			Seq1 181 ASFSQYGAGLDIVAPGVNVQSTYPGSTYASLNGTSMATPHVAGAAALVKQKNPSWSNVQI 240
	~~SUBS_BACLE 101 SVSSIAQGLEWAGNNGMHVANLSLGSPSPSATLEQAVNSATSRGVLVVAA 150~~		\|\|\|\|.\|\|..::\|.\|\|\|\|\|\|.\|\|\|.\|:.\|.\|\|:\|\|\|\|\|\|\|\|\|\|\|.\|\|\|\|\|.:.\|\|::\|.\|\|
	\|::\|:\|\|\|:\|\|\|.\|\|.\|\|:.\|:\|\|\|\|.\|.\|:\|\|\|.\|\|\|.\|.:.\|:\|:\|.\|		Seq2 273 ASFSTYGPEIEISAPGVNVNSTYTGNRYVSLSGTSMATPHVAGVAALVKSRYPSYTNNQI 332
	~~ELYA_BACHD 193 SLASVAQGIEWAINNNMHIINMSLGSTSGSSTLELAVNRANNAGILLVGA 242~~
			Seq1 241 RNHLKNTATSLGSTNLYGSGLVNAEAATR 269
	~~SUBS_BACLE 151 SGNSGAGSISYPARYANAMAVGATDQNNNRASFSQYGAGLDIVAPGVNVQ 200~~		\|..:..\|\|\|.\|\|\|.:\|\|\|:\|\|\|:\|..\|\|:
	:\|\|:\|...::\|\|\|\|\|:..\|\|\|.\|.\|\|\|..\|\|\|\|\|.\|\|..::\|.\|\|\|\|\|\|.		Seq2 333 RQRINQTATYLGSPSLYGNGLVHAGRATQ 361
	~~ELYA_BACHD 243 AGNTGRQGVNYPARYSGVMAVAAVDQNGQRASFSTYGPEIEISAPGVNVN 292~~		</pre>

	~~SUBS_BACLE 201 STYPGSTYASLNGTSMATPHVAGAAALVKQKNPSWSNVQIRNHLKNTATS 250~~
	\|\|\|.\|:.\|.\|\|:\|\|\|\|\|\|\|\|\|\|\|.\|\|\|\|\|.:.\|\|::\|.\|\|\|..:..\|\|\|.
	~~ELYA_BACHD 293 STYTGNRYVSLSGTSMATPHVAGVAALVKSRYPSYTNNQIRQRINQTATY 342~~

	~~SUBS_BACLE 251 LGSTNLYGSGLVNAEAATR 269~~
	\|\|\|.:\|\|\|:\|\|\|:\|..\|\|:
	~~ELYA_BACHD 343 LGSPSLYGNGLVHAGRATQ~~ 361

	Since the two sequences are of different length (see also the answer to next question), it makes the most sense to use the Smith-Waterman algorithm ("local alignment");		Since the two sequences are of different length (see also the answer to next question), one could say that it makes the most sense to use the Smith-Waterman algorithm ("local alignment");
	~~since~~ this ~~would allow~~ the analysis of the differences and similarities in the parts of the sequences which are actually comparable.		this allows the analysis of the differences and similarities to focus on the parts of the sequences which are actually comparable.

	~~Note:~~ However, by using the global alignment alone one can easily see that the sequences are very similar - apart from the missing piece of approximately 90 amino acids at the start.		However, by using the global alignment alone one can easily see that the sequences are very similar, apart from the missing piece of approximately 90 amino acids at the start.
	So in this case, we have learned something extra about the sequences by first making a global alignment.		So in this case, we have learned something extra about the sequences by first making a global alignment.

Henni: /* Q3 */

2026-09-10T14:47:07Z

← Older revision		Revision as of 15:47, 10 September 2026
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	===Q3===		===Q3===

			'''Length:''' 269, '''Identities:''' 176/269 (65.4%), '''Similarities:''' 214/269 (79.6%), '''Gaps:''' 0/269 (0.0%)

	# Length: 269		# Length: 269
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	When two sequences are very similar, as is the case here, there is generally not much difference in the information you get by using local or global alignment.		When two sequences are very similar, as is the case here, there is generally not much difference in the information you get by using local or global alignment.

	===Q4===		===Q4===

Henni: /* Q2 */

2026-09-10T14:43:18Z

← Older revision		Revision as of 15:43, 10 September 2026
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	FASTA format.		FASTA format.

	===Q2===		===Q2.1===
	'''Alignment Score: 860.50'''		'''Alignment Score: 860.50'''

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	Seq2 361 Q 361		Seq2 361 Q 361
	</pre>		</pre>

			===Q2.2===
			The alignment score increased to 916, all other values are unchanged, and the alignment is identical.

	===Q3===		===Q3===

Henni: /* Q2 */

2026-09-10T14:40:19Z

← Older revision		Revision as of 15:40, 10 September 2026
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	===Q2===		===Q2===
			'''Alignment Score: 860.50'''

	# Length: 361		'''Length:''' 361, '''Identities:''' 176/361 (48.8%), '''Similarities:''' 214/361 (59.3%), '''Gaps:''' 92/361 (25.5%)
	~~# Identity~~: 176/361 (48.8%)
	~~# Similarity~~: 214/361 (59.3%)		<pre>
	# Gaps: 92/361 (25.5%)		Seq1 1 ------------------------------------------------------------ 0
	~~# Score: 860.5~~
			Seq2 1 MRQSLKVMVLSTVALLFMANPAAASEEKKEYLIVVEPEEVSAQSVEESYDVDVIHEFEEI 60
	~~SUBS_BACLE~~ 1 -------------------------------------------------- 0
			Seq1 1 --------------------------------AQSVPWGISRVQAPAAHNRGLTGSGVKV 28
	~~ELYA_BACHD 1 MRQSLKVMVLSTVALLFMANPAAASEEKKEYLIVVEPEEVSAQSVEESYD 50~~		:\|:\|\|\|\|\|\|.:....\|\|\|\|\|:.\|:\|.:\|
			Seq2 61 PVIHAELTKKELKKLKKDPNVKAIEKNAEVTISQTVPWGISFINTQQAHNRGIFGNGARV 120
	~~SUBS_BACLE 1~~ ------------------------------------------~~AQSVPWGI 8~~
	:\|:\|\|\|\|\|		Seq1 29 AVLDTGISTHPDLNIRGGASFVPGEPSTQDGNGHGTHVAGTIAALNNSIGVLGVAPSAEL 88
	~~ELYA_BACHD 51 VDVIHEFEEIPVIHAELTKKELKKLKKDPNVKAIEKNAEVTISQTVPWGI 100~~		\|\|\|\|\|\|\|::\|\|\|\|.\|.\|\|\|\|\|:..\|\|\|..\|.\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|:\|
			Seq2 121 AVLDTGIASHPDLRIAGGASFISSEPSYHDNNGHGTHVAGTIAALNNSIGVLGVAPSADL 180
	~~SUBS_BACLE 9 SRVQAPAAHNRGLTGSGVKVAVLDTGISTHPDLNIRGGASFVPGEPSTQD 58~~
	\|.:....\|\|\|\|\|:.\|:\|.:\|\|\|\|\|\|\|\|::\|\|\|\|.\|.\|\|\|\|\|:..\|\|\|..\|		Seq1 89 YAVKVLGASGSGSVSSIAQGLEWAGNNGMHVANLSLGSPSPSATLEQAVNSATSRGVLVV 148
	~~ELYA_BACHD 101 SFINTQQAHNRGIFGNGARVAVLDTGIASHPDLRIAGGASFISSEPSYHD 150~~		\|\|\|\|\|\|..:\|\|\|\|::\|:\|\|\|:\|\|\|.\|\|.\|\|:.\|:\|\|\|\|.\|.\|:\|\|\|.\|\|\|.\|.:.\|:\|:\|
			Seq2 181 YAVKVLDRNGSGSLASVAQGIEWAINNNMHIINMSLGSTSGSSTLELAVNRANNAGILLV 240
	~~SUBS_BACLE 59 GNGHGTHVAGTIAALNNSIGVLGVAPSAELYAVKVLGASGSGSVSSIAQG 108~~
	.\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|:\|\|\|\|\|\|\|..:\|\|\|\|::\|:\|\|\|		Seq1 149 AASGNSGAGSISYPARYANAMAVGATDQNNNRASFSQYGAGLDIVAPGVNVQSTYPGSTY 208
	~~ELYA_BACHD 151 NNGHGTHVAGTIAALNNSIGVLGVAPSADLYAVKVLDRNGSGSLASVAQG 200~~		.\|:\|\|:\|...::\|\|\|\|\|:..\|\|\|.\|.\|\|\|..\|\|\|\|\|.\|\|..::\|.\|\|\|\|\|\|.\|\|\|.\|:.\|
			Seq2 241 GAAGNTGRQGVNYPARYSGVMAVAAVDQNGQRASFSTYGPEIEISAPGVNVNSTYTGNRY 300
	~~SUBS_BACLE 109 LEWAGNNGMHVANLSLGSPSPSATLEQAVNSATSRGVLVVAASGNSGAGS 158~~
	:\|\|\|.\|\|.\|\|:.\|:\|\|\|\|.\|.\|:\|\|\|.\|\|\|.\|.:.\|:\|:\|.\|:\|\|:\|...		Seq1 209 ASLNGTSMATPHVAGAAALVKQKNPSWSNVQIRNHLKNTATSLGSTNLYGSGLVNAEAAT 268
	~~ELYA_BACHD 201 IEWAINNNMHIINMSLGSTSGSSTLELAVNRANNAGILLVGAAGNTGRQG 250~~		.\|\|:\|\|\|\|\|\|\|\|\|\|\|.\|\|\|\|\|.:.\|\|::\|.\|\|\|..:..\|\|\|.\|\|\|.:\|\|\|:\|\|\|:\|..\|\|
			Seq2 301 VSLSGTSMATPHVAGVAALVKSRYPSYTNNQIRQRINQTATYLGSPSLYGNGLVHAGRAT 360
	~~SUBS_BACLE 159 ISYPARYANAMAVGATDQNNNRASFSQYGAGLDIVAPGVNVQSTYPGSTY 208~~
	::\|\|\|\|\|:..\|\|\|.\|.\|\|\|..\|\|\|\|\|.\|\|..::\|.\|\|\|\|\|\|.\|\|\|.\|:.\|		Seq1 269 R 269
	~~ELYA_BACHD 251 VNYPARYSGVMAVAAVDQNGQRASFSTYGPEIEISAPGVNVNSTYTGNRY~~ 300		:
			Seq2 361 Q 361
	~~SUBS_BACLE~~ 209 ~~ASLNGTSMATPHVAGAAALVKQKNPSWSNVQIRNHLKNTATSLGSTNLYG 258~~		</pre>
	.\|\|:\|\|\|\|\|\|\|\|\|\|\|.\|\|\|\|\|.:.\|\|::\|.\|\|\|..:..\|\|\|.\|\|\|.:\|\|\|
	~~ELYA_BACHD 301 VSLSGTSMATPHVAGVAALVKSRYPSYTNNQIRQRINQTATYLGSPSLYG 350~~

	~~SUBS_BACLE 259 SGLVNAEAATR 269~~
	:\|\|\|:\|..\|\|:
	~~ELYA_BACHD 351 NGLVHAGRATQ~~ 361

	===Q3===		===Q3===