Ortho-SSR-Euca - Revision history

Raj at 17:17, 9 February 2013

2013-02-09T17:17:35Z

← Older revision		Revision as of 17:17, 9 February 2013
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	[[Category:Bioinformatics]]		[[:Category:Bioinformatics]]

	=News SSRs Pipeline Target=		=News SSRs Pipeline Target=

Raj at 17:17, 9 February 2013

2013-02-09T17:17:09Z

← Older revision		Revision as of 17:17, 9 February 2013
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			[[Category:Bioinformatics]]

	=News SSRs Pipeline Target=		=News SSRs Pipeline Target=
	* Designing Multiplex SSR primers from E. camaldulensis, E. grandis and E. globulus available [http://eucalyptusdb.bi.up.ac.za/ EucalyptusDB] and NCBI sources		* Designing Multiplex SSR primers from E. camaldulensis, E. grandis and E. globulus available [http://eucalyptusdb.bi.up.ac.za/ EucalyptusDB] and NCBI sources
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	=== Manuscript ===		=== Manuscript ===

	~~[[:Category:Bioinformatics]]~~

Raj at 04:10, 10 August 2012

2012-08-10T04:10:49Z

← Older revision		Revision as of 04:10, 10 August 2012
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	=== Manuscript ===		=== Manuscript ===

	[[Category:Bioinformatics]]		[[:Category:Bioinformatics]]

Raj: /* Strategy */

2010-01-07T14:34:06Z

Strategy

← Older revision		Revision as of 14:34, 7 January 2010
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	* Design multiplex primers (to save 3 folds of time and money) marking the repeat region		* Design multiplex primers (to save 3 folds of time and money) marking the repeat region
	* Validate the primers on E. camal experimentally.		* Validate the primers on E. camal experimentally.

	=Implementation=		=Implementation=
	* EST from E.globulus: total 13468		* EST from E.globulus: total 13468

Raj: /* Primer Design */

2010-01-04T10:26:58Z

Primer Design

← Older revision		Revision as of 10:26, 4 January 2010
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	print OUT "PRIMER_MAX_SIZE = 23\n";		print OUT "PRIMER_MAX_SIZE = 23\n";
	print OUT "PRIMER_NUM_RETURN = 1\n";		print OUT "PRIMER_NUM_RETURN = 1\n";
	print OUT "PRIMER_PRODUCT_SIZE_RANGE=90-~~320~~\n";		print OUT "PRIMER_PRODUCT_SIZE_RANGE=90-300\n";
	</pre>		</pre>
	* Results		* Results

Raj: /* Primer Design */

2010-01-04T10:13:59Z

Primer Design

← Older revision		Revision as of 10:13, 4 January 2010
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	===Primer Design===		===Primer Design===
	* Param		* Param
	** print OUT "PRIMER_MIN_GC = 49\n";		<pre>
	** print OUT "PRIMER_MAX_GC = 55\n";		print OUT "PRIMER_MIN_GC = 49\n";
	** print OUT "PRIMER_OPT_GC = 50\n";		print OUT "PRIMER_MAX_GC = 55\n";
	** print OUT "PRIMER_MIN_TM = 59\n";		print OUT "PRIMER_OPT_GC = 50\n";
	** print OUT "PRIMER_MAX_TM = 63\n";		print OUT "PRIMER_MIN_TM = 59\n";
	** print OUT "PRIMER_OPT_TM = 61\n";		print OUT "PRIMER_MAX_TM = 63\n";
	** print OUT "PRIMER_OPT_SIZE = 22\n";		print OUT "PRIMER_OPT_TM = 61\n";
	** print OUT "PRIMER_MIN_SIZE = 21\n";		print OUT "PRIMER_OPT_SIZE = 22\n";
	** print OUT "PRIMER_MAX_SIZE = 23\n";		print OUT "PRIMER_MIN_SIZE = 21\n";
	** print OUT "PRIMER_NUM_RETURN = 1\n";		print OUT "PRIMER_MAX_SIZE = 23\n";
	** print OUT "PRIMER_PRODUCT_SIZE_RANGE=90-320\n";		print OUT "PRIMER_NUM_RETURN = 1\n";
			print OUT "PRIMER_PRODUCT_SIZE_RANGE=90-320\n";
			</pre>
	* Results		* Results
	** Total: 211 CAMAL: 63 pairs GRAN: pairs		** Total: 211 CAMAL: 63 pairs GRAN: pairs

Raj: /* Primer Design */

2010-01-04T10:12:42Z

Primer Design

← Older revision		Revision as of 10:12, 4 January 2010
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	* Results		* Results
	** Total: 211 CAMAL: 63 pairs GRAN: pairs		** Total: 211 CAMAL: 63 pairs GRAN: pairs
	* ~~Follwing~~ filters were applied manually on the above results		* Following filters were applied manually on the above results
	** Pick up 4 equal ranges from camal and grandis		** Pick up 4 equal ranges from camal and grandis
	** Ignore primer pairs based on high difference in For/Rev Tm value		** Ignore primer pairs based on high difference in For/Rev Tm value
	** Type of Repeats in the primer		** Type of Repeats in the primer
			** Remove the A/T at the 3' end
			** Co-ordinates showing the same repeats
	** ePCR positive ness		** ePCR positive ness
	Final: Total: '''''' CAMAL: '''''' pairs GRAN: '''''' pairs		Final: Total: '''''' CAMAL: '''''' pairs GRAN: '''''' pairs
	* M13 added to 5' END of forward		* M13 added to 5' END of forward

	===Oligo Synthesis ===		===Oligo Synthesis ===
	* Pilot plan: 20 primer pairs (CAMAL 10 and GRAN 10)		* Pilot plan: 20 primer pairs (CAMAL 10 and GRAN 10)

Raj: /* = Manuscript */

2010-01-04T10:10:12Z

= Manuscript

← Older revision		Revision as of 10:10, 4 January 2010
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	* Final list of validated primers:		* Final list of validated primers:

	=== Manuscript ==		=== Manuscript ===

	[[Category:Bioinformatics]]		[[Category:Bioinformatics]]

Raj: /* =Validation */

2010-01-04T10:09:20Z

=Validation

← Older revision		Revision as of 10:09, 4 January 2010
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	* Pilot plan: 20 primer pairs (CAMAL 10 and GRAN 10)		* Pilot plan: 20 primer pairs (CAMAL 10 and GRAN 10)
	* Results: Success rate:		* Results: Success rate:
	===Validation==		===Validation===
	* E. camal Template:		* E. camal Template:
	* Final list of validated primers:		* Final list of validated primers:

	=== Manuscript ==		=== Manuscript ==

	[[Category:Bioinformatics]]		[[Category:Bioinformatics]]

Raj: /* Primer Design */

2010-01-04T10:08:57Z

Primer Design

← Older revision		Revision as of 10:08, 4 January 2010
Line 121:		Line 121:

	===Primer Design===		===Primer Design===
	* ~~Single Plex~~		* Param
	** ~~Issue: Designing with the broader range 100~~-~~350 thows more into higher side~~		** print OUT "PRIMER_MIN_GC = 49\n";
	** ~~Strategy~~: ~~4 ranges indenpendent pipeline~~ : ~~100-150 \| 160 210 \| 220-270 \| 280-330~~		** print OUT "PRIMER_MAX_GC = 55\n";
	*** Pick up 4 equal ranges from camal and grandis		** print OUT "PRIMER_OPT_GC = 50\n";
	*** Ignore primer pairs based on high difference in For/Rev Tm value		** print OUT "PRIMER_MIN_TM = 59\n";
	*** Type of Repeats in the primer		** print OUT "PRIMER_MAX_TM = 63\n";
	*** ePCR positive ness		** print OUT "PRIMER_OPT_TM = 61\n";
	* ~~Multiplex~~		** print OUT "PRIMER_OPT_SIZE = 22\n";
	** '''~~PrimerPlex~~''' ~~Dependency~~		** print OUT "PRIMER_MIN_SIZE = 21\n";
			** print OUT "PRIMER_MAX_SIZE = 23\n";
			** print OUT "PRIMER_NUM_RETURN = 1\n";
			** print OUT "PRIMER_PRODUCT_SIZE_RANGE=90-320\n";
			* Results
			** Total: 211 CAMAL: 63 pairs GRAN: pairs
			* Follwing filters were applied manually on the above results
			** Pick up 4 equal ranges from camal and grandis
			** Ignore primer pairs based on high difference in For/Rev Tm value
			** Type of Repeats in the primer
			** ePCR positive ness
			Final: Total: '''''' CAMAL: '''''' pairs GRAN: '''''' pairs
			* M13 added to 5' END of forward
			===Oligo Synthesis ===
			* Pilot plan: 20 primer pairs (CAMAL 10 and GRAN 10)
			* Results: Success rate:
			===Validation==
			* E. camal Template:
			* Final list of validated primers:
			=== Manuscript ==

	[[Category:Bioinformatics]]		[[Category:Bioinformatics]]