phpSSRMiner: Simple Sequence Repeat Marker Miner

phpSSRMiner: Simple Sequence Repeat Marker Miner (v0.9b)

phpSSRMiner effectively streamlines the process of SSR (Simple Sequence Repeat) identification, primer design, and in-silicon primer verification in a single web interface. Sequences are managed in different libraries. SSRs and primers are searchable in different manners.

Click the "View" button under end user's column for result searching and viewing. If you wish to access Designer's Workspace of the phpssrminer, please contact the Zhao Bioinformatics Lab, Samuel Roberts Noble Foundation. We will send you a web link allowing you to access "Designers" functions for sequence management, SSR detection, primer design and in-silicon PCR validation, etc; and administrator functions for library management.

Library	Description	Time In	End User
1	Noble Foundation Tall Fescue Tentative Unigenes Assembled by TIGR (9 Libraries) Festuca arundinacea Taxonomy ID: 4606 Rank: species Genetic code: Translation table 1 (Standard) Mitochondrial genetic code: Translation table 1 (Standard) Other names: synonym: Schedonorus arundinaceus synonym: Lolium arundinaceum synonym: Schedonorus phoenix (Scop.) Holub synonym: Schedonorus phoenix synonym: Lolium arundinaceum (Schreb.) Darbysh. synonym: Schedonorus arundinaceus (Schreb.) Dumort. synonym: Festuca arundinacea Schreb. synonym: Festuca elatior L. synonym: Festuca elatior common name: tall fescue	2006-01-10 14:35:53
2	Tea DT1 Unigenes Tea DT1 Unigenes	2006-01-30 13:21:01
5	Switchgrass Unigenes (assemblied from 11, 990 ESTs Downloaded from NCBI EST database on 01-20-2007, ID range: DN140629-DN152624, missing six IDs) Panicum virgatum Taxonomy ID: 38727 Genbank common name: switchgrass Rank: species Genetic code: Translation table 1 (Standard) Mitochondrial genetic code: Translation table 1 (Standard) Lineage( full ) About the switchgrass Unigenes: Among total 7, 066 switchgrass Unigenes , there are 5, 322 Singlet ESTs and 1, 744 contigs assemblied from 6, 668 ESTs.	2007-01-23 09:32:57
4	Tea 2043 Unigenes Tea 2043 Unigenes	2006-02-21 15:32:12
9	nf_white_clover_atg_library NF White Clover Genomics Sequences (ATG Library)	2007-03-14 11:02:19
10	nf_white_clover_atg_and_ga_library NF White Clover Genomics Sequences (Non-redundant sequences over ATG and GA libraries)	2007-03-14 11:38:42
11	NF White Clover Genomics Sequences (CA Library) NEW Taxon: Trifolium repens L. Genus: Trifolium, subgenus: Trifolium, section: Trifoliastrum Family: Fabaceae (alt. Leguminosae), subfamily: Faboideae, tribe: Trifolieae. Also placed in: Papilionaceae Nomen number: 300625 subordinate taxa: Trifolium repens var. biasolettii Trifolium repens var. giganteum Trifolium repens var. latum Trifolium repens var. macrorrhizum Trifolium repens var. pallescens Trifolium repens var. repens Common names: white clover Note: This library contains cDNA insertion sequences targeting CA-rich regions.	2007-04-25 13:28:50
12	NF White Clover Genomics Sequences (ATG Library) NEW Taxon: Trifolium repens L. Genus: Trifolium, subgenus: Trifolium, section: Trifoliastrum Family: Fabaceae (alt. Leguminosae), subfamily: Faboideae, tribe: Trifolieae. Also placed in: Papilionaceae Nomen number: 300625 subordinate taxa: Trifolium repens var. biasolettii Trifolium repens var. giganteum Trifolium repens var. latum Trifolium repens var. macrorrhizum Trifolium repens var. pallescens Trifolium repens var. repens Common names: white clover Note: This library contains cDNA insertion sequences targeting ATG-rich regions.	2007-04-25 13:57:59
6	Yongzhen Tea Genomics Sequence 02-16-2007 Yongzhen Tea Genomics Sequence 02-16-2007	2007-02-16 17:17:31
7	NF White Clover Genomics Sequences (CA Library) NF White Clover Genomics Sequences (CA Library)	2007-02-26 16:39:48
8	ncbi_white_clover NCBI's white clover sequences as of 20070226	2007-02-28 10:04:56
13	NF White Clover Genomics Sequences (CA and ATG Libraries) NEW Taxon: Trifolium repens L. Genus: Trifolium, subgenus: Trifolium, section: Trifoliastrum Family: Fabaceae (alt. Leguminosae), subfamily: Faboideae, tribe: Trifolieae. Also placed in: Papilionaceae Nomen number: 300625 subordinate taxa: Trifolium repens var. biasolettii Trifolium repens var. giganteum Trifolium repens var. latum Trifolium repens var. macrorrhizum Trifolium repens var. pallescens Trifolium repens var. repens Common names: white clover Note: This is the set of non-redundant sequences assembled from the CA libraries and ATG libraries.	2007-04-27 10:20:53
14	GenBank White Clover Nucleotide Sequences Originally 1844 sequences downloaded on 06/05/2007 with query '"Trifolium repens" [Organism]'. 107 sequences duplicate to NF CA / ATG libraries (with BLASTN e-value 1e-20) are removed. 1737 sequences are stored here.	2007-06-05 16:02:51
15	NF White Clover CA Library (NEW 06/25/2007) Taxon: Trifolium repens L. Genus: Trifolium, subgenus: Trifolium, section: Trifoliastrum Family: Fabaceae (alt. Leguminosae), subfamily: Faboideae, tribe: Trifolieae. Also placed in: Papilionaceae Nomen number: 300625 subordinate taxa: Trifolium repens var. biasolettii Trifolium repens var. giganteum Trifolium repens var. latum Trifolium repens var. macrorrhizum Trifolium repens var. pallescens Trifolium repens var. repens Common names: white clover Note: This library contains cDNA insertion sequences targeting CA-rich regions.	2007-06-25 09:47:15
16	NF White Clover ATG Library (NEW 06/25/2007) Taxon: Trifolium repens L. Genus: Trifolium, subgenus: Trifolium, section: Trifoliastrum Family: Fabaceae (alt. Leguminosae), subfamily: Faboideae, tribe: Trifolieae. Also placed in: Papilionaceae Nomen number: 300625 subordinate taxa: Trifolium repens var. biasolettii Trifolium repens var. giganteum Trifolium repens var. latum Trifolium repens var. macrorrhizum Trifolium repens var. pallescens Trifolium repens var. repens Common names: white clover Note: This library contains cDNA insertion sequences targeting ATG-rich regions.	2007-06-25 13:50:11
17	NF White Clover CA + ATG Library (NEW 06/25/2007) Taxon: Trifolium repens L. Genus: Trifolium, subgenus: Trifolium, section: Trifoliastrum Family: Fabaceae (alt. Leguminosae), subfamily: Faboideae, tribe: Trifolieae. Also placed in: Papilionaceae Nomen number: 300625 subordinate taxa: Trifolium repens var. biasolettii Trifolium repens var. giganteum Trifolium repens var. latum Trifolium repens var. macrorrhizum Trifolium repens var. pallescens Trifolium repens var. repens Common names: white clover Note: This is the set of non-redundant sequences assembled from the CA libraries and ATG libraries.	2007-06-25 16:15:16
18	GenBank White Clover Nucleotide Sequences (NEW 06/25/2007) Originally 1844 sequences downloaded on 06/05/2007 with query '"Trifolium repens" [Organism]'. 104 sequences duplicate to NF CA / ATG libraries (with BLASTN e-value 1e-20) are removed. 1740 sequences are stored here.	2007-06-25 16:23:53
19	NF White Clover ATG Library (New Batch, 2008/01/15) Taxon: Trifolium repens L. Genus: Trifolium, subgenus: Trifolium, section: Trifoliastrum Family: Fabaceae (alt. Leguminosae), subfamily: Faboideae, tribe: Trifolieae. Also placed in: Papilionaceae Nomen number: 300625 subordinate taxa: Trifolium repens var. biasolettii Trifolium repens var. giganteum Trifolium repens var. latum Trifolium repens var. macrorrhizum Trifolium repens var. pallescens Trifolium repens var. repens Common names: white clover Note: This library contains cDNA insertion sequences targeting ATG-rich regions.	2008-01-16 10:38:02
20	NF White Clover CA Library (New Batch, 2008/01/15) Taxon: Trifolium repens L. Genus: Trifolium, subgenus: Trifolium, section: Trifoliastrum Family: Fabaceae (alt. Leguminosae), subfamily: Faboideae, tribe: Trifolieae. Also placed in: Papilionaceae Nomen number: 300625 subordinate taxa: Trifolium repens var. biasolettii Trifolium repens var. giganteum Trifolium repens var. latum Trifolium repens var. macrorrhizum Trifolium repens var. pallescens Trifolium repens var. repens Common names: white clover Note: This library contains cDNA insertion sequences targeting CA-rich regions.	2008-01-16 11:07:34
21	NF White Clover ATG + CA Library (New Batch, 2008/01/15) Taxon: Trifolium repens L. Genus: Trifolium, subgenus: Trifolium, section: Trifoliastrum Family: Fabaceae (alt. Leguminosae), subfamily: Faboideae, tribe: Trifolieae. Also placed in: Papilionaceae Nomen number: 300625 subordinate taxa: Trifolium repens var. biasolettii Trifolium repens var. giganteum Trifolium repens var. latum Trifolium repens var. macrorrhizum Trifolium repens var. pallescens Trifolium repens var. repens Common names: white clover Note: This is the non-redundant sequence library over CA and ATG libraries that are sequenced in 2008.	2008-01-16 11:44:14
22	NF White Clover ATG Library (Sequences from 2007 and 2008) Taxon: Trifolium repens L. Genus: Trifolium, subgenus: Trifolium, section: Trifoliastrum Family: Fabaceae (alt. Leguminosae), subfamily: Faboideae, tribe: Trifolieae. Also placed in: Papilionaceae Nomen number: 300625 subordinate taxa: Trifolium repens var. biasolettii Trifolium repens var. giganteum Trifolium repens var. latum Trifolium repens var. macrorrhizum Trifolium repens var. pallescens Trifolium repens var. repens Common names: white clover Note: This library contains cDNA insertion sequences targeting ATG-rich regions.	2008-01-16 13:12:28
23	NF White Clover CA Library (Sequences from 2007 and 2008) Taxon: Trifolium repens L. Genus: Trifolium, subgenus: Trifolium, section: Trifoliastrum Family: Fabaceae (alt. Leguminosae), subfamily: Faboideae, tribe: Trifolieae. Also placed in: Papilionaceae Nomen number: 300625 subordinate taxa: Trifolium repens var. biasolettii Trifolium repens var. giganteum Trifolium repens var. latum Trifolium repens var. macrorrhizum Trifolium repens var. pallescens Trifolium repens var. repens Common names: white clover Note: This library contains cDNA insertion sequences targeting CA-rich regions.	2008-01-16 15:10:30
24	NF White Clover ATG + CA Library (2007 & 2008) Taxon: Trifolium repens L. Genus: Trifolium, subgenus: Trifolium, section: Trifoliastrum Family: Fabaceae (alt. Leguminosae), subfamily: Faboideae, tribe: Trifolieae. Also placed in: Papilionaceae Nomen number: 300625 subordinate taxa: Trifolium repens var. biasolettii Trifolium repens var. giganteum Trifolium repens var. latum Trifolium repens var. macrorrhizum Trifolium repens var. pallescens Trifolium repens var. repens Common names: white clover Note: This is the non-redundant sequence library over CA and ATG libraries that are sequenced in 2007 and 2008.	2008-01-16 15:56:07
25	GenBank White Clover Nucleotide Sequences 20080117 Originally 3566 sequences downloaded on 01/17/2008 with query '"Trifolium repens" [Organism]'. 1583 sequences that were submitted by NF were removed. 102 sequences duplicate to current NF CA / ATG consensus (with BLASTN e-value 1e-20 and bit score 200) are removed. 1881 sequences are stored here.	2008-01-21 13:28:32
26	Unigenes assemblied from ESTs in Medicago sativa(Alfalfa) Trichomes	2008-02-12 10:15:14
27	In-silico SSR screen in 2455 white lupin (Lupinus albus L.) unigenes assembled from total 5150 ESTs Taxonomy ID: 3870 Genbank common name: white lupine Rank: species Genetic code: Translation table 1 (Standard) Mitochondrial genetic code: Translation table 1 (Standard) Other names: Lupinus albus L.	2008-04-22 10:05:13