Two Eel Scaffolds - Revision history

Rf at 14:21, 24 May 2016

2016-05-24T14:21:25Z

Rf at 13:19, 24 May 2016

2016-05-24T13:19:26Z

Rf at 23:00, 22 May 2016

2016-05-22T23:00:41Z

Rf at 21:28, 15 May 2016

2016-05-15T21:28:05Z

Rf at 21:11, 15 May 2016

2016-05-15T21:11:04Z

Rf at 21:10, 15 May 2016

2016-05-15T21:10:57Z

Rf at 21:09, 15 May 2016

2016-05-15T21:09:18Z

Rf at 21:07, 15 May 2016

2016-05-15T21:07:13Z

Rf at 20:50, 15 May 2016

2016-05-15T20:50:25Z

Rf: /* pdcd10b's 7 exons against eelScaffold32 */

2016-05-15T16:18:11Z

‎pdcd10b's 7 exons against eelScaffold32

Show changes

@@ Line 161: / Line 161: @@
 After checking, these two hits refer to the same tilapia transcript and to the same gene, ENSONIG00000001157 or pdcd10b.
-And for EelScaffold320, we get:
+And for EelScaffold320 and zebrafish CDS, we get:
   g10.t1	ENSONIT00000001474.1	82.78	395	64	4	206	598	545	937	5e-95	  350

@@ Line 151: / Line 151: @@
 In order to visually navigate the results of these annotations, they can be viewed on a browser [http://stab.st-andrews.ac.uk/JBrowse-1.12.1 here].
-Against zebrafish, EelScaffold320 gives 19 predicted genes while EelScaffold32 give 39. We can llok through some of these. We blast against zebrafish CDS, and in EelScaffold32 we get:
+Against zebrafish, EelScaffold320 gives 19 predicted genes while EelScaffold32 give 39. We can look through these by a strigent blast against zebrafish CDS. We get:
   g16.t1	ENSONIT00000001464.1	84.98	293	44	0	152	444	266	558	6e-80	  298
-which is pdcd10b.
+Against lamprey, we suspect that the best hits will be the same:
 And for EelScaffold320, we get:
@@ Line 163: / Line 167: @@
   g19.t1	ENSONIT00000005827.1	88.66	494	56	0	1	494	55	548	6e-172	  603
-Against lamprey, we suspect that the best hits will be the same. For EelScaffold32:
+So this time, despite being a smaller sequence, three genes come up.
 As can be expected with the strong match for pdcd10b in EelScaffold, the '''ENSONIT00000001464''' transcript does indeed match with '''ENSONIG00000001157''' which is '''pdcd10b'''.

@@ Line 151: / Line 151: @@
 In order to visually navigate the results of these annotations, they can be viewed on a browser [http://stab.st-andrews.ac.uk/JBrowse-1.12.1 here].
-Against zebrafish, EelScaffold320 gives 19 predicted genes while EelScaffold32 give 39. An exhaustive search through each of these would require more time, but we can certainly undertake a quick blast with very stringent matching targets against the '''tilapia'' CDS to see if any of these stand out.
+Against zebrafish, EelScaffold320 gives 19 predicted genes while EelScaffold32 give 39. We can llok through some of these. We blast against zebrafish CDS, and in EelScaffold32 we get:
-In the case of EelScaffold32 against zebrafish  we get:
+  g16.t1	ENSONIT00000001464.1	84.98	293	44	0	152	444	266	558	6e-80	  298
- g16.t1	ENSONIT00000001464.1	84.98	293	44	0	152	444	266	558	6e-80	  298
+which is pdcd10b.
 And for EelScaffold320, we get:

← Older revision		Revision as of 21:28, 15 May 2016
Line 172:		Line 172:
	g8.t1 ENSONIT00000005855.1 82.95 651 105 5 51 698 21 668 1e-165 582		g8.t1 ENSONIT00000005855.1 82.95 651 105 5 51 698 21 668 1e-165 582
	g10.t1 ENSONIT00000005827.1 88.51 522 60 0 3 524 27 548 0.0 632		g10.t1 ENSONIT00000005827.1 88.51 522 60 0 3 524 27 548 0.0 632
		+
		+	As can be expected with the strong match for pdcd10b in EelScaffold, the '''ENSONIT00000001464''' transcript does indeed match with '''ENSONIG00000001157''' which is '''pdcd10b'''.

@@ Line 11: / Line 11: @@
 * '''eelScaffold32''' contains any part of [http://www.ensembl.org/Oreochromis_niloticus/Gene/Summary?g=ENSONIG00000001157&db=core PDCD10b] (Programmed cell death 10b).
 * '''eelScaffold320''' contains any part of [http://www.ensembl.org/Oreochromis_niloticus/Gene/Summary?g=ENSONIG00000001167&db=core nrd1a] (Nardilysin, N-arginine dibasic convertase)
 = Detecting presence of '''pdcd10b''' and '''nrd1a''' =

← Older revision		Revision as of 21:10, 15 May 2016
Line 12:		Line 12:
	* '''eelScaffold320''' contains any part of [http://www.ensembl.org/Oreochromis_niloticus/Gene/Summary?g=ENSONIG00000001167&db=core nrd1a] (Nardilysin, N-arginine dibasic convertase)		* '''eelScaffold320''' contains any part of [http://www.ensembl.org/Oreochromis_niloticus/Gene/Summary?g=ENSONIG00000001167&db=core nrd1a] (Nardilysin, N-arginine dibasic convertase)

−	~~= Gene Predictor =~~
−
−	~~One of the most up-to-date (2016) gene predictors is Augustus. It uses HMM profiles based on a related organism. In terms of eel, there are two given organisms: Zebra fish ('''zb''') and Lamprey~~
−	~~('''lp''') which Augustus makes available. Though ''tilapia'' is not available, it is possible - given time - to train and establish HMM profile for this organism.~~
−
−	~~An example Augustus command line is as follows:~~
−
−	~~augustus --species=lamprey eelScaffold320.fa >aug_s320_lp.gtf~~
−
−	~~Augustus outputs in the GTF format, for future visual browsing on JBrowse, we need to convert to the related format, GFF:~~
−
−	~~gtf2gff.pl --printExon --gff3 < aug_s32_lp.gtf --out=aug_s32_lp.gff~~
−
−	~~We are also probably interested in the CDS and proteins sequences of the predicted genes, we can use the following Augustus-supplied script:~~
−
−	~~getAnnoFasta.pl --seqfile=eelScaffold32.fa aug_s32_lp.gtf~~
−
−	~~In order to visually navigate the results of these annotations, they can be viewed on a browser [http://stab.st-andrews.ac.uk/JBrowse-1.12.1 here].~~
−
−	Against zebrafish, EelScaffold320 gives 19 predicted genes while EelScaffold32 give 39. An exhaustive search through each of these would require more time, but we can certainly undertake a quick blast with very stringent matching targets against the '''tilapia'' CDS to see if any of these stand out.
−
−	~~In the case of EelScaffold32 against zebrafish we get:~~
−
−	~~g16.t1 ENSONIT00000001464.1 84.98 293 44 0 152 444 266 558 6e-80 298~~
−
−	~~And for EelScaffold320, we get:~~
−
−	~~g10.t1 ENSONIT00000001474.1 82.78 395 64 4 206 598 545 937 5e-95 350~~
−	~~g11.t1 ENSONIT00000005855.1 82.95 651 105 5 42 689 21 668 1e-165 582~~
−	~~g19.t1 ENSONIT00000005827.1 88.66 494 56 0 1 494 55 548 6e-172 603~~
−
−	~~Against lamprey, we suspect that the best hits will be the same. For EelScaffold32:~~
−
−	~~g6.t1 ENSONIT00000001464.1 84.88 291 44 0 199 489 268 558 4e-79 294~~
−
−	~~And for EelScaffold320, we get:~~
−
−	~~g7.t1 ENSONIT00000001474.1 81.57 510 90 4 134 641 611 1118 7e-116 418~~
−	~~g8.t1 ENSONIT00000005855.1 82.95 651 105 5 51 698 21 668 1e-165 582~~
−	~~g10.t1 ENSONIT00000005827.1 88.51 522 60 0 3 524 27 548 0.0 632~~


Line 173:		Line 133:

	This is a more complicated gene, so the alignment is less good, but there is clearly good identity so we can reasonably suspect the reverse strand harbours this second gene.		This is a more complicated gene, so the alignment is less good, but there is clearly good identity so we can reasonably suspect the reverse strand harbours this second gene.
		+
		+	= Gene Predictor =
		+
		+	One of the most up-to-date (2016) gene predictors is Augustus. It uses HMM profiles based on a related organism. In terms of eel, there are two given organisms: Zebra fish ('''zb''') and Lamprey
		+	('''lp''') which Augustus makes available. Though ''tilapia'' is not available, it is possible - given time - to train and establish HMM profile for this organism.
		+
		+	An example Augustus command line is as follows:
		+
		+	augustus --species=lamprey eelScaffold320.fa >aug_s320_lp.gtf
		+
		+	Augustus outputs in the GTF format, for future visual browsing on JBrowse, we need to convert to the related format, GFF:
		+
		+	gtf2gff.pl --printExon --gff3 < aug_s32_lp.gtf --out=aug_s32_lp.gff
		+
		+	We are also probably interested in the CDS and proteins sequences of the predicted genes, we can use the following Augustus-supplied script:
		+
		+	getAnnoFasta.pl --seqfile=eelScaffold32.fa aug_s32_lp.gtf
		+
		+	In order to visually navigate the results of these annotations, they can be viewed on a browser [http://stab.st-andrews.ac.uk/JBrowse-1.12.1 here].
		+
		+	Against zebrafish, EelScaffold320 gives 19 predicted genes while EelScaffold32 give 39. An exhaustive search through each of these would require more time, but we can certainly undertake a quick blast with very stringent matching targets against the '''tilapia'' CDS to see if any of these stand out.
		+
		+	In the case of EelScaffold32 against zebrafish we get:
		+
		+	g16.t1 ENSONIT00000001464.1 84.98 293 44 0 152 444 266 558 6e-80 298
		+
		+	And for EelScaffold320, we get:
		+
		+	g10.t1 ENSONIT00000001474.1 82.78 395 64 4 206 598 545 937 5e-95 350
		+	g11.t1 ENSONIT00000005855.1 82.95 651 105 5 42 689 21 668 1e-165 582
		+	g19.t1 ENSONIT00000005827.1 88.66 494 56 0 1 494 55 548 6e-172 603
		+
		+	Against lamprey, we suspect that the best hits will be the same. For EelScaffold32:
		+
		+	g6.t1 ENSONIT00000001464.1 84.88 291 44 0 199 489 268 558 4e-79 294
		+
		+	And for EelScaffold320, we get:
		+
		+	g7.t1 ENSONIT00000001474.1 81.57 510 90 4 134 641 611 1118 7e-116 418
		+	g8.t1 ENSONIT00000005855.1 82.95 651 105 5 51 698 21 668 1e-165 582
		+	g10.t1 ENSONIT00000005827.1 88.51 522 60 0 3 524 27 548 0.0 632

@@ Line 21: / Line 21: @@
   augustus --species=lamprey eelScaffold320.fa >aug_s320_lp.gtf
-Augustus outputs in the GTF format, for visual browsing on JBrowse, we need to convert to the related format, GFF:
+Augustus outputs in the GTF format, for future visual browsing on JBrowse, we need to convert to the related format, GFF:
   gtf2gff.pl --printExon --gff3 < aug_s32_lp.gtf --out=aug_s32_lp.gff
 Against zebrafish, EelScaffold320 gives 19 predicted genes while EelScaffold32 give 39. An exhaustive search through each of these would require more time, but we can certainly undertake a quick blast with very stringent matching targets against the '''tilapia'' CDS to see if any of these stand out.
@@ Line 43: / Line 49: @@
 And for EelScaffold320, we get:
-We are also probably interested in the CDS and proteins sequences of the predicted genes, we can use the follown Augustus-supplied script:
+ g7.t1   ENSONIT00000001474.1    81.57   510 90  4   134 641 611 1118    7e-116    418
+ g8.t1   ENSONIT00000005855.1    82.95   651 105 5   51  698 21  668 1e-165    582
-  getAnnoFasta.pl --seqfile=eelScaffold32.fa aug_s32_lp.gtf
+  g10.t1  ENSONIT00000005827.1    88.51   522 60  0   3   524 27  548 0.0   632
 = Detecting presence of '''pdcd10b''' and '''nrd1a''' =

← Older revision		Revision as of 21:07, 15 May 2016
Line 37:		Line 37:
	g19.t1 ENSONIT00000005827.1 88.66 494 56 0 1 494 55 548 6e-172 603		g19.t1 ENSONIT00000005827.1 88.66 494 56 0 1 494 55 548 6e-172 603

		+	Against lamprey, we suspect that the best hits will be the same. For EelScaffold32:

		+	g6.t1 ENSONIT00000001464.1 84.88 291 44 0 199 489 268 558 4e-79 294

		+	And for EelScaffold320, we get:

	We are also probably interested in the CDS and proteins sequences of the predicted genes, we can use the follown Augustus-supplied script:		We are also probably interested in the CDS and proteins sequences of the predicted genes, we can use the follown Augustus-supplied script:

← Older revision		Revision as of 20:50, 15 May 2016
Line 24:		Line 24:

	gtf2gff.pl --printExon --gff3 < aug_s32_lp.gtf --out=aug_s32_lp.gff		gtf2gff.pl --printExon --gff3 < aug_s32_lp.gtf --out=aug_s32_lp.gff
		+
		+	Against zebrafish, EelScaffold320 gives 19 predicted genes while EelScaffold32 give 39. An exhaustive search through each of these would require more time, but we can certainly undertake a quick blast with very stringent matching targets against the '''tilapia'' CDS to see if any of these stand out.
		+
		+	In the case of EelScaffold32 against zebrafish we get:
		+
		+	g16.t1 ENSONIT00000001464.1 84.98 293 44 0 152 444 266 558 6e-80 298
		+
		+	And for EelScaffold320, we get:
		+
		+	g10.t1 ENSONIT00000001474.1 82.78 395 64 4 206 598 545 937 5e-95 350
		+	g11.t1 ENSONIT00000005855.1 82.95 651 105 5 42 689 21 668 1e-165 582
		+	g19.t1 ENSONIT00000005827.1 88.66 494 56 0 1 494 55 548 6e-172 603
		+
		+
		+

	We are also probably interested in the CDS and proteins sequences of the predicted genes, we can use the follown Augustus-supplied script:		We are also probably interested in the CDS and proteins sequences of the predicted genes, we can use the follown Augustus-supplied script: