GcatWiki - Recent changes [en]

Blasting Spacers for Haloferax mediterranei

Karicheson — Thu, 19 Nov 2009 17:08:42 GMT

Special:Log/upload

Karicheson — Thu, 19 Nov 2009 17:08:24 GMT

uploaded "[[Image:HMED6.jpg]]"

Special:Log/upload

Karicheson — Thu, 19 Nov 2009 17:08:13 GMT

uploaded "[[Image:HMED4.jpg]]"

Special:Log/upload

Karicheson — Thu, 19 Nov 2009 17:08:02 GMT

uploaded "[[Image:HMED3.jpg]]"

Special:Log/upload

Karicheson — Thu, 19 Nov 2009 17:07:52 GMT

uploaded "[[Image:HMED2.jpg]]"

Special:Log/upload

Karicheson — Thu, 19 Nov 2009 17:07:42 GMT

uploaded "[[Image:HMED1.jpg]]"

Blasting Spacers for Haloferax mediterranei

Karicheson — Thu, 19 Nov 2009 17:07:32 GMT

New page

[[Image:HMED1.jpg]]

[[Image:HMED2.jpg]]

[[Image:HMED3.jpg]]

[[Image:HMED4.jpg]]

[[Image:HMED5.jpg]]

CRISPR info

Karicheson — Thu, 19 Nov 2009 17:02:15 GMT

Halomicrobium mukohataei Genome Fall 2009

Karicheson — Thu, 19 Nov 2009 16:54:50 GMT

(Difference between revisions)

Special:Log/upload

Karicheson — Thu, 19 Nov 2009 16:53:14 GMT

uploaded "[[Image:Powerpoint.ppt]]"

Halomicrobium mukohataei Genome Fall 2009

Karicheson — Thu, 19 Nov 2009 16:53:00 GMT

(Difference between revisions)

Davidson Missouri W/Davidson Protocols

MaCampbell — Wed, 18 Nov 2009 16:14:59 GMT

Mycobacterium phage Virus Hit from Spacer 5 in Crispr Two: Blast Alignment to Other Halophiles

Karicheson — Wed, 18 Nov 2009 05:30:23 GMT

Burkholderia phage Virus Hit from Spacer 14 in Crispr One: Blast Alignment to Other Halophiles

Karicheson — Wed, 18 Nov 2009 05:28:15 GMT

Special:Log/upload

Karicheson — Wed, 18 Nov 2009 05:23:52 GMT

uploaded "[[Image:OurspeciesOne.jpg]]"

Archaeal BJ1 Virus Hit from Spacer 2 in Crispr One: Blast Alignments to Other Halophiles

Karicheson — Wed, 18 Nov 2009 05:23:43 GMT

Mycobacterium phage Virus Hit from Spacer 5 in Crispr Two: Blast Alignment to Other Halophiles

Karicheson — Wed, 18 Nov 2009 05:12:30 GMT

Burkholderia phage Virus Hit from Spacer 14 in Crispr One: Blast Alignment to Other Halophiles

Karicheson — Wed, 18 Nov 2009 05:09:45 GMT

Archaeal BJ1 Virus Hit from Spacer 2 in Crispr One: Blast Alignments to Other Halophiles

Karicheson — Wed, 18 Nov 2009 05:04:23 GMT

Special:Log/upload

Karicheson — Wed, 18 Nov 2009 05:02:12 GMT

uploaded "[[Image:Question2.jpg]]"

Special:Log/upload

Karicheson — Wed, 18 Nov 2009 05:02:01 GMT

uploaded "[[Image:Question.jpg]]"

Haloarcula sinaiiensis: Blast Results

Karicheson — Wed, 18 Nov 2009 05:01:46 GMT

Special:Log/upload

Karicheson — Wed, 18 Nov 2009 05:00:03 GMT

uploaded "[[Image:Virus1insertions4.jpg]]"

Haloarcula sinaiiensis: Blast Results

Karicheson — Wed, 18 Nov 2009 04:59:46 GMT

Special:Log/upload

Karicheson — Wed, 18 Nov 2009 04:58:28 GMT

uploaded "[[Image:Virus1insertions3.jpg]]"

Haloarcula sinaiiensis: Blast Results

Karicheson — Wed, 18 Nov 2009 04:58:17 GMT

Special:Log/upload

Karicheson — Wed, 18 Nov 2009 04:56:34 GMT

uploaded "[[Image:Virus1insertions2.jpg]]"

Haloarcula sinaiiensis: Blast Results

Karicheson — Wed, 18 Nov 2009 04:56:16 GMT

Special:Log/upload

Karicheson — Wed, 18 Nov 2009 04:53:13 GMT

uploaded "[[Image:Virus1insertions.jpg]]"

Haloarcula sinaiiensis: Blast Results

Karicheson — Wed, 18 Nov 2009 04:52:59 GMT

Archaeal BJ1 Virus Hit from Spacer 2 in Crispr One: Blast Alignments to Other Halophiles

Karicheson — Wed, 18 Nov 2009 04:39:35 GMT

Spacers for Other Species

Karicheson — Wed, 18 Nov 2009 04:36:23 GMT

Special:Log/upload

Karicheson — Wed, 18 Nov 2009 04:36:11 GMT

uploaded "[[Image:HSCRISPR2.jpg]]"

Special:Log/upload

Karicheson — Wed, 18 Nov 2009 04:35:57 GMT

uploaded "[[Image:HSCRISPR1.jpg]]"

Spacers for Other Species

Karicheson — Wed, 18 Nov 2009 04:35:42 GMT

Special:Log/upload

Karicheson — Wed, 18 Nov 2009 04:11:35 GMT

uploaded "[[Image:HUCRISPR4.jpg]]"

Special:Log/upload

Karicheson — Wed, 18 Nov 2009 04:11:21 GMT

uploaded "[[Image:HUCRISPR3.jpg]]"

Special:Log/upload

Karicheson — Wed, 18 Nov 2009 04:11:09 GMT

uploaded "[[Image:HUCRISPR2.jpg]]"

Special:Log/upload

Karicheson — Wed, 18 Nov 2009 04:10:55 GMT

uploaded "[[Image:HUCRISPR1.jpg]]"

Spacers for Other Species

Karicheson — Wed, 18 Nov 2009 04:09:55 GMT

 [[Spacers for Other Species]]
+[[Blasting Spacers for Haloferax mediterranei]]
 [[CRISPR-associated Proteins]]

 # [http://www.bio.davidson.edu/courses/molbio/labnotebook.html How to Keep a Lab Notebook]
 # [http://www.bio.davidson.edu/courses/Molbio/Protocols/reagents.html Common molecular reagents]
+# [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC106306/pdf/am002240.pdf Using degradation tags on proteins such as GFP]
 # [http://parts.mit.edu/registry/index.php/Assembly:Standard_assembly Standard Assembly]
 # [http://partsregistry.org/Help:BioBrick_Prefix_and_Suffix BioBrick Ends]

Revision as of 05:30, 18 November 2009		Current revision
Line 12:		Line 12:

	[[Image:virus35.jpg]]		[[Image:virus35.jpg]]
		+
		+
		+
		+	Blasted viral genome against our genome and got no hits within spacers!!!!!!!!!!!!???????????
		+

Revision as of 05:28, 18 November 2009		Current revision
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	Our species does not show up because different parameters for short sequence when we blasted the spacer		Our species does not show up because different parameters for short sequence when we blasted the spacer
		+
		+
		+
		+
		+	Blasted our species and got some hits but no hits of spacers sharing similarity with this virus. . . that is because of the different parameters??????????
		+
		+

 Blastn Alignment: Query= viral (Accession Number: AM419438.1) and Subject=species of choice
+OUR SPECIES:  Accession Number: NC_013202
+Below are the hits which insert with spacers in our species genome:
+Only see one hit with the virus in one of the spacers in our species. . . aka this virus to our knowledge only inserts into one spacer. . . Note that it only inserts in the spacer region and not the DR region and that the spacer it inserts in corresponds with the blasted spacer that gave this virus as a hit
+[[Image:ourspeciesOne.jpg]]
 ----

Revision as of 17:08, 19 November 2009		Current revision
Line 7:		Line 7:
	[[Image:HMED4.jpg]]		[[Image:HMED4.jpg]]

-	[[Image:HMED5.jpg]]	+	[[Image:HMED6.jpg]]

Revision as of 05:12, 18 November 2009		Current revision
Line 40:		Line 40:

	[[Haloarcula sinaiiensis Blasting Results for Virus 3]]		[[Haloarcula sinaiiensis Blasting Results for Virus 3]]
		+
		+	CONCLUSION: this virus did not insert into this species' spacers

 Halorhabdus utahensis:  Accession number determined from NCBI: NC_013158.1
+CONCLUSION: these viral hits are not in spacers. . . this virus did not enter spacer in this species
 [[Image:Virus2HU.jpg]]
 Haloarcula sinaiiensis
+CONCLUSION: this virus did not insert into the spacers of this species
 [[Image:virus2H1.jpg]]

 [[Haloarcula sinaiiensis: Blast Results]]
+CONCLUSION: found viral insertions of this virus in some of the spacers
 didnt accept anything above 0.009
 blast recall number: G5RXZPH1113

 In spacer 12 of cripsr 2
+[[Image:question.jpg]]
+[[Image:question2.jpg]]
+spans whole crispr????

 In spacer 14 of crispr 2
+[[Image:virus1insertions4.jpg]]
+In spacer 12 of cripsr 2

 In spacer 20 of crispr 2- NOTE it extends into DR section
+[[Image:virus1insertions3.jpg]]
+In spacer 14 of crispr 2

 Blast results that are in spacers in this species:
 ----
-[[Image:viral1insertions.jpg]]
+[[Image:virus1insertions.jpg]]
 In spacers 15 and 14 respectively of crispr 2
+[[Image:virus1insertions2.jpg]]
+In spacer 20 of crispr 2- NOTE it extends into DR section

 ----
+CONCLUSION: THESE ''VIRAL INSERTIONS ARE NOT INTO SPACERS IN THIS SPECIES'': aligned spacer number with the significant hits below
 '''Halorhabdus utahensis''':  Accession number determined from NCBI: NC_013158.1

 '''Halorhabdus utahensis'''
-I confirmed CRISPR:
+confirmed CRISPR:
 [[Image:HSCRISPR1.jpg]]

 '''Halorhabdus utahensis'''
-[[Image:HUCRISPR1.jpg]]
+I confirmed CRISPR:
-[[Image:HUCRISPR2.jpg]]
+[[Image:HSCRISPR1.jpg]]
-[[Image:HUCRISPR3.jpg]]
+[[Image:HSCRISPR2.jpg]]
-[[Image:HUCRISPR4.jpg]]
+No confirmed CRISPRs
+No confirmed CRISPRs
 '''Haloarcula sinaiiensis'''
+[[Image:HUCRISPR1.jpg]]
+[[Image:HUCRISPR2.jpg]]
+[[Image:HUCRISPR3.jpg]]
+[[Image:HUCRISPR4.jpg]]