SSR discovery - Revision history

Appbio at 06:25, 19 March 2013

2013-03-19T06:25:43Z

Appbio at 02:09, 3 July 2012

2012-07-03T02:09:08Z

Appbio at 02:08, 3 July 2012

2012-07-03T02:08:37Z

Appbio at 03:16, 6 April 2012

2012-04-06T03:16:41Z

Appbio at 02:25, 10 February 2011

2011-02-10T02:25:38Z

Appbio at 02:25, 10 February 2011

2011-02-10T02:25:26Z

Appbio at 02:25, 10 February 2011

2011-02-10T02:25:07Z

Appbio at 02:24, 10 February 2011

2011-02-10T02:24:18Z

Appbio at 04:40, 4 February 2011

2011-02-04T04:40:29Z

Appbio at 11:10, 19 September 2010

2010-09-19T11:10:13Z

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 The rapid expansion in the availability of sequence data enables the identification of genes and markers underlying key traits for application in molecular breeding and germplasm enhancement. When SSRs are derived from Expressed Sequence Tags (ESTs), they become gene specific. These features make EST-SSRs highly valuable markers for the construction and comparison of genetic maps. The development of SSRs has traditionally been limited by the time consuming and labour intensive requirement to construct, enrich and sequence genomic libraries. However, the identification of SSRs from expressed sequences, produced during gene discovery projects, provides a rich source of valuable molecular markers. Furthermore, these sequences, and the markers developed from them, are a valuable resource for comparative genomic studies.
-Previously we have applied the tool [http://flora.acpfg.com.au/ssrprimer2/ SSRPrimer] for the rapid discovery of Simple Sequence Repeats (SSRs) from bulk sequence data (Robinson et al., 2004) and from all sequences in Genbank using [http://appliedbioinformatics.com.au/projects/ssrtaxonomy/php/index.php SSRTaxonomy Tree] (Jewell et al., 2006). SSRPrimer combines Sputnik, a program to identify SSRs in the sequence, with Primer3, to design PCR primers for amplifying the SSR. SSRTaxonomy Tree applies this tool on a species wide scale. While these tools enables the rapid and cost effective discovery of SSRs, laboratory assessment is still required to measure their polymorphic status and therefore their applicability to genetic studies. The in silico enrichment of discovered SSRs, for those likely to be polymorphic, would save considerable expense in laboratory assessment through reducing the number of interrogation primers designed to monomorphic SSRs. We have therefore developed a tool for the in silico identification of polymorphic SSRs from assembled redundant expressed sequences.
+Previously we have applied the tool [http://www.appliedbioinformatics.com.au/projects/ssrPrimer/ SSRPrimer] for the rapid discovery of Simple Sequence Repeats (SSRs) from bulk sequence data (Robinson et al., 2004) and from all sequences in Genbank using [http://appliedbioinformatics.com.au/projects/ssrtaxonomy/php/index.php SSRTaxonomy Tree] (Jewell et al., 2006). SSRPrimer combines Sputnik, a program to identify SSRs in the sequence, with Primer3, to design PCR primers for amplifying the SSR. SSRTaxonomy Tree applies this tool on a species wide scale. While these tools enables the rapid and cost effective discovery of SSRs, laboratory assessment is still required to measure their polymorphic status and therefore their applicability to genetic studies. The in silico enrichment of discovered SSRs, for those likely to be polymorphic, would save considerable expense in laboratory assessment through reducing the number of interrogation primers designed to monomorphic SSRs. We have therefore developed a tool for the in silico identification of polymorphic SSRs from assembled redundant expressed sequences.
 ===Tools===
-[http://flora.acpfg.com.au/ssrprimer2/ SSRPrimer]
+[http://www.appliedbioinformatics.com.au/projects/ssrPrimer/ SSRPrimer]
 [http://appliedbioinformatics.com.au/projects/ssrtaxonomy/php/index.php SSRTaxonomy Tree]

← Older revision		Revision as of 02:09, 3 July 2012
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	[http://appliedbioinformatics.com.au/projects/ssrtaxonomy/php/index.php SSRTaxonomy Tree]		[http://appliedbioinformatics.com.au/projects/ssrtaxonomy/php/index.php SSRTaxonomy Tree]

−	[SSRPoly]	+	[[SSRPoly]]

← Older revision		Revision as of 02:08, 3 July 2012
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	[http://appliedbioinformatics.com.au/projects/ssrtaxonomy/php/index.php SSRTaxonomy Tree]		[http://appliedbioinformatics.com.au/projects/ssrtaxonomy/php/index.php SSRTaxonomy Tree]
		+
		+	[SSRPoly]

← Older revision		Revision as of 03:16, 6 April 2012
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−	===Back to [[~~research~~\|~~research projects~~]]===	+	===Back to [[Main_Page\|main page]]===

← Older revision		Revision as of 02:25, 10 February 2011
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	[http://appliedbioinformatics.com.au/projects/ssrtaxonomy/php/index.php SSRTaxonomy Tree]		[http://appliedbioinformatics.com.au/projects/ssrtaxonomy/php/index.php SSRTaxonomy Tree]
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	===References:===		===References:===

← Older revision		Revision as of 02:25, 10 February 2011
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	[http://flora.acpfg.com.au/ssrprimer2/ SSRPrimer]		[http://flora.acpfg.com.au/ssrprimer2/ SSRPrimer]
		+
	[http://appliedbioinformatics.com.au/projects/ssrtaxonomy/php/index.php SSRTaxonomy Tree]		[http://appliedbioinformatics.com.au/projects/ssrtaxonomy/php/index.php SSRTaxonomy Tree]

← Older revision		Revision as of 02:24, 10 February 2011
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	Previously we have applied the tool [http://flora.acpfg.com.au/ssrprimer2/ SSRPrimer] for the rapid discovery of Simple Sequence Repeats (SSRs) from bulk sequence data (Robinson et al., 2004) and from all sequences in Genbank using [http://appliedbioinformatics.com.au/projects/ssrtaxonomy/php/index.php SSRTaxonomy Tree] (Jewell et al., 2006). SSRPrimer combines Sputnik, a program to identify SSRs in the sequence, with Primer3, to design PCR primers for amplifying the SSR. SSRTaxonomy Tree applies this tool on a species wide scale. While these tools enables the rapid and cost effective discovery of SSRs, laboratory assessment is still required to measure their polymorphic status and therefore their applicability to genetic studies. The in silico enrichment of discovered SSRs, for those likely to be polymorphic, would save considerable expense in laboratory assessment through reducing the number of interrogation primers designed to monomorphic SSRs. We have therefore developed a tool for the in silico identification of polymorphic SSRs from assembled redundant expressed sequences.		Previously we have applied the tool [http://flora.acpfg.com.au/ssrprimer2/ SSRPrimer] for the rapid discovery of Simple Sequence Repeats (SSRs) from bulk sequence data (Robinson et al., 2004) and from all sequences in Genbank using [http://appliedbioinformatics.com.au/projects/ssrtaxonomy/php/index.php SSRTaxonomy Tree] (Jewell et al., 2006). SSRPrimer combines Sputnik, a program to identify SSRs in the sequence, with Primer3, to design PCR primers for amplifying the SSR. SSRTaxonomy Tree applies this tool on a species wide scale. While these tools enables the rapid and cost effective discovery of SSRs, laboratory assessment is still required to measure their polymorphic status and therefore their applicability to genetic studies. The in silico enrichment of discovered SSRs, for those likely to be polymorphic, would save considerable expense in laboratory assessment through reducing the number of interrogation primers designed to monomorphic SSRs. We have therefore developed a tool for the in silico identification of polymorphic SSRs from assembled redundant expressed sequences.
		+
		+
		+	===Tools===
		+
		+	==[http://flora.acpfg.com.au/ssrprimer2/ SSRPrimer]==
		+	[http://appliedbioinformatics.com.au/projects/ssrtaxonomy/php/index.php SSRTaxonomy Tree

	===References:===		===References:===

@@ Line 1: / Line 1: @@
 Molecular genetic markers represent one of the most powerful tools for the analysis of plant genomes and the association of heritable traits with underlying genetic variation. One form of sequence based marker, Simple Sequence Repeats (SSRs), also known as microsatellites, now predominate applications in modern plant genetic analysis and are one of the most powerful genetic markers. The reducing cost of DNA sequencing and increasing availability of large sequence data sets permits the mining of this data for large numbers of SSRs. These may then be used in applications such as genetic linkage analysis and trait mapping, diversity analysis, association studies, and marker assisted selection.
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 * Burgess B, Mountford H, Hopkins CJ, Love C, Ling AE, Spangenberg G, Edwards D and Batley J. (2006) Identification and characterisation of Simple Sequence Repeat (SSR) markers derived in silico from Brassica oleracea genome shotgun sequences. [http://onlinelibrary.wiley.com/doi/10.1111/j.1471-8286.2006.01488.x/abstract Molecular Ecology Notes 6: 1191-1194]
 * Keniry A, Hopkins CJ, Jewell E, Morrison B, Spangenberg GS, Edwards D and Batley J. (2006) Identification and characterisation of Simple Sequence Repeat (SSR) markers from Fragaria x ananassa expressed sequences. [http://onlinelibrary.wiley.com/doi/10.1111/j.1471-8286.2005.01215.x/abstract Molecular Ecology Notes 6: 319-322]
+* Mortimer J, Batley J, Love C, Logan E and Edwards D. (2005) Simple Sequence Repeat (SSR) and GC distribution in the Arabidopsis thaliana genome. Journal of Plant Biotechnology 7: 17-25