SNParrayDB - Revision history

Dave: /* Link */

2018-11-26T09:47:40Z

‎Link

ArminPS: /* Using SNParrayDB */

2018-02-07T08:30:59Z

‎Using SNParrayDB

ArminPS: /* Using SNParrayDB */

2018-02-07T08:30:35Z

‎Using SNParrayDB

ArminPS: /* Using SNParrayDB */

2018-02-07T08:29:57Z

‎Using SNParrayDB

ArminPS: /* Using SNParrayDB */

2018-02-07T08:28:36Z

‎Using SNParrayDB

ArminPS: /* Using SNParrayDB */

2018-02-07T08:25:53Z

‎Using SNParrayDB

ArminPS: /* Using SNParrayDB */

2018-02-07T08:25:32Z

‎Using SNParrayDB

ArminPS: /* Scan a genomic region for SNPs */

2018-02-07T08:21:26Z

‎Scan a genomic region for SNPs

ArminPS: /* Using SNParrayDB */

2018-02-07T08:19:21Z

‎Using SNParrayDB

ArminPS: /* Scan a genomic region for SNPs */

2018-02-07T08:14:47Z

‎Scan a genomic region for SNPs

@@ Line 3: / Line 3: @@
 ==Link==
-The Crop SNParrayDB can be accessed here: http://snpdb.appliedbioinformatics.com.au:5000/
+The Crop SNParrayDB can be accessed here: http://snpdb.appliedbioinformatics.com.au/
 ==Using SNParrayDB==

@@ Line 9: / Line 9: @@
 ===Scan a genomic region for SNPs===
 A comparative search query between the cultivars Karat and Marnoo for SNPs in a region of chromosome A01 can be carried out from the landing page, by inputting species, lines, chromosome and coordinates (Fig. 1).
-[[File:CropSNPdb_Search.png|200px|thumb|'''Figure 1''' Overview of the Search page for querying SNPs]]
+[[File:CropSNPdb_Search.png|200px|thumb|right|'''Figure 1''' Overview of the Search page for querying SNPs]]
 The search result is dumped to the screen in tabular format. Additional information on the SNP can be accessed by clicking on the SNP row, which brings up a pop-up box with all additional SNP metadata (Fig. 2).

@@ Line 9: / Line 9: @@
 ===Scan a genomic region for SNPs===
 A comparative search query between the cultivars Karat and Marnoo for SNPs in a region of chromosome A01 can be carried out from the landing page, by inputting species, lines, chromosome and coordinates (Fig. 1).
-[[File:CropSNPdb_Search.png|50px|thumb|right|'''Figure 1''' Overview of the Search page for querying SNPs]]
+[[File:CropSNPdb_Search.png|200px|thumb|'''Figure 1''' Overview of the Search page for querying SNPs]]
 The search result is dumped to the screen in tabular format. Additional information on the SNP can be accessed by clicking on the SNP row, which brings up a pop-up box with all additional SNP metadata (Fig. 2).
-[[File:Mypic.png|50px|thumb|right|'''Figure 2''' Result of an example search for SNPs between the oilseed rape lines Karat and Marnoo]]
+[[File:Mypic.png|200px|thumb|right|'''Figure 2''' Result of an example search for SNPs between the oilseed rape lines Karat and Marnoo]]
 ===Bulk download SNPs by chromosome===
 Users can download all canola genotypes hosted by the database by chromosome as comma-delimited tabular files (Fig. 3).
-[[File:CropSNPdb_Download.png|50px|thumb|right|'''Figure 3''' Download page of Crop SNParrayDB]]
+[[File:CropSNPdb_Download.png|200px|thumb|right|'''Figure 3''' Download page of Crop SNParrayDB]]
 ===Submit SNPs===
 User can upload their own oilseed rape SNP array data using the submission portal of Crop SNParrayDB (Fig.4). A genotype matrix and a list of line names and accessions should be uploaded. Example files with correct formatting can be downloaded from the page.
-[[File:CropSNPdb_Submit.png|50px|thumb|right|'''Figure 4''' Submission portal of Crop SNParrayDB]]
+[[File:CropSNPdb_Submit.png|200px|thumb|right|'''Figure 4''' Submission portal of Crop SNParrayDB]]
 ===References===

@@ Line 9: / Line 9: @@
 ===Scan a genomic region for SNPs===
 A comparative search query between the cultivars Karat and Marnoo for SNPs in a region of chromosome A01 can be carried out from the landing page, by inputting species, lines, chromosome and coordinates (Fig. 1).
-[[File:CropSNPdb_Search.png|200px|thumb|right|'''Figure 1''' Overview of the Search page for querying SNPs]]
+[[File:CropSNPdb_Search.png|50px|thumb|right|'''Figure 1''' Overview of the Search page for querying SNPs]]
 The search result is dumped to the screen in tabular format. Additional information on the SNP can be accessed by clicking on the SNP row, which brings up a pop-up box with all additional SNP metadata (Fig. 2).
-[[File:Mypic.png|200px|thumb|right|'''Figure 2''' Result of an example search for SNPs between the oilseed rape lines Karat and Marnoo]]
+[[File:Mypic.png|50px|thumb|right|'''Figure 2''' Result of an example search for SNPs between the oilseed rape lines Karat and Marnoo]]
 ===Bulk download SNPs by chromosome===
 Users can download all canola genotypes hosted by the database by chromosome as comma-delimited tabular files (Fig. 3).
-[[File:CropSNPdb_Download.png|200px|thumb|right|'''Figure 3''' Download page of Crop SNParrayDB]]
+[[File:CropSNPdb_Download.png|50px|thumb|right|'''Figure 3''' Download page of Crop SNParrayDB]]
 ===Submit SNPs===
 User can upload their own oilseed rape SNP array data using the submission portal of Crop SNParrayDB (Fig.4). A genotype matrix and a list of line names and accessions should be uploaded. Example files with correct formatting can be downloaded from the page.
-[[File:CropSNPdb_Submit.png|200px|thumb|right|'''Figure 4''' Submission portal of Crop SNParrayDB]]
+[[File:CropSNPdb_Submit.png|50px|thumb|right|'''Figure 4''' Submission portal of Crop SNParrayDB]]
 ===References===

@@ Line 12: / Line 12: @@
 The search result is dumped to the screen in tabular format. Additional information on the SNP can be accessed by clicking on the SNP row, which brings up a pop-up box with all additional SNP metadata (Fig. 2).
-[[File:Mypic.png|200px|thumb|right|'''Figure 2''' Result of an example search for SNPs between the canola lines Karat and Marnoo]]
+[[File:Mypic.png|200px|thumb|right|'''Figure 2''' Result of an example search for SNPs between the oilseed rape lines Karat and Marnoo]]
 ===Bulk download SNPs by chromosome===
-[Section in progress]
+Users can download all canola genotypes hosted by the database by chromosome as comma-delimited tabular files (Fig. 3).
 [[File:CropSNPdb_Download.png|200px|thumb|right|'''Figure 3''' Download page of Crop SNParrayDB]]
 ===Submit SNPs===
 [[File:CropSNPdb_Submit.png|200px|thumb|right|'''Figure 4''' Submission portal of Crop SNParrayDB]]
@@ Line 26: / Line 27: @@
 *Xu LP, Hu KN, Zhang ZQ, Guan CY, Chen S, Hua W, Li JN, Wen J, Yi B, Shen JX, et al. 2016. Genome-wide association study reveals the genetic architecture of flowering time in rapeseed (Brassica napus L.). DNA Research 23(1): 43-52.
 *The Triticeae Toolbox (T3) (http://triticeaetoolbox.org/)

← Older revision		Revision as of 08:25, 7 February 2018
Line 26:		Line 26:
	*Xu LP, Hu KN, Zhang ZQ, Guan CY, Chen S, Hua W, Li JN, Wen J, Yi B, Shen JX, et al. 2016. Genome-wide association study reveals the genetic architecture of flowering time in rapeseed (Brassica napus L.). DNA Research 23(1): 43-52.		*Xu LP, Hu KN, Zhang ZQ, Guan CY, Chen S, Hua W, Li JN, Wen J, Yi B, Shen JX, et al. 2016. Genome-wide association study reveals the genetic architecture of flowering time in rapeseed (Brassica napus L.). DNA Research 23(1): 43-52.
	*The Triticeae Toolbox (T3) (http://triticeaetoolbox.org/)		*The Triticeae Toolbox (T3) (http://triticeaetoolbox.org/)
		+
		+
		+
		+
		+
		+
		+
		+
		+
		+
		+
		+
		+

@@ Line 12: / Line 12: @@
 The search result is dumped to the screen in tabular format. Additional information on the SNP can be accessed by clicking on the SNP row, which brings up a pop-up box with all additional SNP metadata.
-[[File:CropSNPdb_Result.png|200px|thumb|right|Result of an example search for SNPs between the canola lines Karat and Marnoo]]
+[[File:Mypic.png|200px|thumb|right|Result of an example search for SNPs between the canola lines Karat and Marnoo]]
 ===Bulk download SNPs by chromosome===

@@ Line 8: / Line 8: @@
 ===Scan a genomic region for SNPs===
-An example of a comparative search query between the cultivars Karat and Marnoo for SNPs in a region of chromosome A01 is provided.
+A comparative search query between the cultivars Karat and Marnoo for SNPs in a region of chromosome A01 can be carried out from the landing page, by inputting species, lines, chromosome and coordinates.
-[[File:CropSNPdb_Search.png|200px|thumb|right|alt text]]
+[[File:CropSNPdb_Search.png|200px|thumb|right|Overview of the Search page for querying SNPs]]
 The search result is dumped to the screen in tabular format. Additional information on the SNP can be accessed by clicking on the SNP row, which brings up a pop-up box with all additional SNP metadata.
-[[File:CropSNPdb_Result.png|200px|thumb|right|alt text]]
+[[File:CropSNPdb_Result.png|200px|thumb|right|Result of an example search for SNPs between the canola lines Karat and Marnoo]]
 ===Bulk download SNPs by chromosome===