JP Feb 23 16 - Revision history

Jupreziosi at 19:56, 23 February 2016

2016-02-23T19:56:52Z

2016-02-23T19:56:20Z

2016-02-23T19:56:06Z

2016-02-23T19:54:27Z

2016-02-23T19:47:08Z

2016-02-23T19:46:28Z

2016-02-23T19:38:25Z

2016-02-23T19:22:25Z

2016-02-23T19:02:25Z

2016-02-23T18:48:10Z

← Older revision		Revision as of 19:56, 23 February 2016
Line 24:		Line 24:

	Cloud blast packages the sequences in group of ~50. Used the 10 results setting.		Cloud blast packages the sequences in group of ~50. Used the 10 results setting.
		+

	Used the protein database as the search forum (PDB).		Used the protein database as the search forum (PDB).

@@ Line 20: / Line 20: @@
 Used cloud blast on the 3596 proteins of unknown function.
 "Save Results" should be in a folder. It produces many zip files when it packages them for blasting.
 Cloud blast packages the sequences in group of ~50. Used the 10 results setting.
 Used the protein database as the search forum (PDB).
 Went very fast. Like 2 minutes. Then mapped and annotated.
 / 3596 now have annotations. There's an error in exporting just these genes to a new file. 187 are fully annotated (Blue).
 Cloud blast from reference data base taking much longer (REF) ~25 minutes.
 We found 1078 / 3596 with this method. 356 are fully annotated. 488 green and blue.
 We took both fully annotated lists (GAF Files) and gave them to Dylan's group.

@@ Line 17: / Line 17: @@
-GO TERMS:
+GO TERMS: CLOUD BLAST
 Used cloud blast on the 3596 proteins of unknown function.
 "Save Results" should be in a folder. It produces many zip files when it packages them for blasting.
 Cloud blast packages the sequences in group of ~50. Used the 10 results setting.
 Used the protein database as the search forum (PDB).
 Went very fast. Like 2 minutes. Then mapped and annotated.
 Cloud blast from reference data base taking much longer (REF) ~25 minutes.
 We found 1078 / 3596 with this method. 356 are fully annotated. 488 green and blue.
 We took both fully annotated lists (GAF Files) and gave them to Dylan's group.

@@ Line 24: / Line 24: @@
 Went very fast. Like 2 minutes. Then mapped and annotated.
-/ 3596 now have annotations. There's an error in exporting just these genes to a new file. 187 are fully annotated.
+/ 3596 now have annotations. There's an error in exporting just these genes to a new file. 187 are fully annotated (Blue).
 Cloud blast from reference data base taking much longer (REF) ~25 minutes.

@@ Line 24: / Line 24: @@
 Went very fast. Like 2 minutes. Then mapped and annotated.
-/ 3596 now have annotations. There's an error in exporting just these genes. 187 are fully annotated.
+/ 3596 now have annotations. There's an error in exporting just these genes to a new file. 187 are fully annotated.
 Cloud blast from reference data base taking much longer (REF) ~25 minutes.
 We found 1078 / 3596 with this method. 356 are fully annotated. 488 green and blue.

← Older revision		Revision as of 19:38, 23 February 2016
Line 23:		Line 23:
	Went very fast. Like 2 minutes. Then mapped and annotated.		Went very fast. Like 2 minutes. Then mapped and annotated.

−	254 / 3596 now have annotations. There's an error in ~~extracting~~ just these genes. 187 are fully annotated.	+	254 / 3596 now have annotations. There's an error in exporting just these genes. 187 are fully annotated.
		+
		+	Cloud blast from reference data base taking much longer (nr) ~25 minutes.

← Older revision		Revision as of 19:22, 23 February 2016
Line 22:		Line 22:
	Cloud blast packages the sequences in group of ~50. Used the 10 results setting. Used the protein database as the search forum.		Cloud blast packages the sequences in group of ~50. Used the 10 results setting. Used the protein database as the search forum.
	Went very fast. Like 2 minutes. Then mapped and annotated.		Went very fast. Like 2 minutes. Then mapped and annotated.
		+
		+	254 / 3596 now have annotations. There's an error in extracting just these genes. 187 are fully annotated.

← Older revision		Revision as of 19:02, 23 February 2016
Line 15:		Line 15:

	Graphics as figures, methods section. Each group writes their own paper. Need a new game plan moving forward.		Graphics as figures, methods section. Each group writes their own paper. Need a new game plan moving forward.
		+
		+
		+	GO TERMS:
		+	Used cloud blast on the 3596 proteins of unknown function.
		+	"Save Results" should be in a folder. It produces many zip files when it packages them for blasting.
		+	Cloud blast packages the sequences in group of ~50. Used the 10 results setting. Used the protein database as the search forum.
		+	Went very fast. Like 2 minutes. Then mapped and annotated.

← Older revision		Revision as of 18:48, 23 February 2016
Line 13:		Line 13:
	* Find genes differentially regulated b/t fed and nonfed; that are differentially expressed at the beginning of the cascade.		* Find genes differentially regulated b/t fed and nonfed; that are differentially expressed at the beginning of the cascade.
	* May have to chase individual genes to find a good candidate gene.		* May have to chase individual genes to find a good candidate gene.
		+
		+	Graphics as figures, methods section. Each group writes their own paper. Need a new game plan moving forward.