GenDBWiki/WebDocumentation/DialogWindows/PatScan - Revision history

Admin: 22 revisions

2011-10-26T06:18:22Z

22 revisions

← Older revision	Revision as of 08:18, 26 October 2011
(No difference)

imported>RobertSchmieder at 14:42, 28 March 2006

2006-03-28T14:42:13Z

← Older revision		Revision as of 16:42, 28 March 2006
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	The result shows the name of the region which the match belongs to, the position in the contig and the distance to the start of the region.		The result shows the name of the region which the match belongs to, the position in the contig and the distance to the start of the region.
	Every row has on its far right a link to the [[GenDBWiki/WebDocumentation/DialogWindows/AnnotationDialog\|AnnotationDialog]]. Sometimes its handy to annotate ~~all~~ matches at once without clicking on every rows annotate link.		Every row has on its far right a link to the [[GenDBWiki/WebDocumentation/DialogWindows/AnnotationDialog\|AnnotationDialog]]. Sometimes its handy to annotate few matches at once without clicking on every rows annotate link.
	For that reason there is a button ~~alled~~ '''~~batch annotate~~''' which opens the [[GenDBWiki/WebDocumentation/DialogWindows/MultiAnnotator\|MultiAnnotator]] to annotated many regions at once.		For that reason there is a button called '''"Annotate selection"''' which opens the [[GenDBWiki/WebDocumentation/DialogWindows/MultiAnnotator\|MultiAnnotator]] to annotated many regions at once.

	~~You can see that we~~ specified a offset of 100 bases and filtered all matches which lie within the bounds of a region. As a result we get all intergenic matches which start at maximum 100 bases infront of a region. This can be very handy for identifying promotor regions.		We specified a offset of 100 bases and filtered all matches which lie within the bounds of a region. As a result we get all intergenic matches which start at maximum 100 bases infront of a region. This can be very handy for identifying promotor regions.

	== Exporter for Results ==		== Exporter for Results ==

imported>RobertSchmieder at 14:36, 28 March 2006

2006-03-28T14:36:20Z

← Older revision		Revision as of 16:36, 28 March 2006
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	You can choose the values, which should be exported, by clicking in the associated checkboxes.		You can choose the values, which should be exported, by clicking in the associated checkboxes.
			Beneath this, there is a checkbox for adding a ''comment line'' to the export-file, which contains the name of the checked values.
	You also can choose the type of separation between '''"tabulator"''' (recommended) and '''"comma"'''.		You also can choose the type of separation between '''"tabulator"''' (recommended) and '''"comma"'''.

imported>RobertSchmieder at 14:31, 28 March 2006

2006-03-28T14:31:54Z

← Older revision		Revision as of 16:31, 28 March 2006
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	[[Image:GenDBWiki$$WebDocumentation$$DialogWindows$$PatScan$PatScan_b2.png]]		[[Image:GenDBWiki$$WebDocumentation$$DialogWindows$$PatScan$PatScan_b2.png]]

	~~===~~ This feature is available since GenDB version 2.4. ~~===~~		'''This feature is available since GenDB version 2.4.'''
	The exporter for the results of the pattern search is shown after clicking the '''Show exporting fields''' button. This button is only visible next to the '''Annotate''' button, if your status allows you to export data.
			The exporter for the results of the pattern search is shown after clicking the '''"Show exporting fields"''' button. This button is only visible next to the '''"Annotate"''' button, if your status allows you to export data.

	You can choose the values, which should be exported, by clicking in the associated checkboxes.		You can choose the values, which should be exported, by clicking in the associated checkboxes.
	You also can choose the type of separation between '''tabulator''' (recommended) and '''comma'''.		You also can choose the type of separation between '''"tabulator"''' (recommended) and '''"comma"'''.
	By clicking the '''Export values''' button, the export-file will be generated and a save dialog will be opened.
			By clicking the '''"Export values"''' button, the export-file will be generated and a save dialog will be opened.

	== Q/A Troubleshooting ==		== Q/A Troubleshooting ==

imported>RobertSchmieder at 14:29, 28 March 2006

2006-03-28T14:29:34Z

← Older revision		Revision as of 16:29, 28 March 2006
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	[[Image:GenDBWiki$$WebDocumentation$$DialogWindows$$PatScan$PatScan_b2.png]]		[[Image:GenDBWiki$$WebDocumentation$$DialogWindows$$PatScan$PatScan_b2.png]]

	===This feature is available since GenDB version 2.4.===		=== This feature is available since GenDB version 2.4. ===
	The exporter for the results of the pattern search is shown after clicking the '''Show exporting fields''' button. This button is only visible next to the '''Annotate''' button, if your status allows you to export data.		The exporter for the results of the pattern search is shown after clicking the '''Show exporting fields''' button. This button is only visible next to the '''Annotate''' button, if your status allows you to export data.
	You can choose the values, which should be exported, by clicking in the associated checkboxes.		You can choose the values, which should be exported, by clicking in the associated checkboxes.

imported>RobertSchmieder at 14:29, 28 March 2006

2006-03-28T14:29:03Z

← Older revision		Revision as of 16:29, 28 March 2006
Line 63:		Line 63:
	[[Image:GenDBWiki$$WebDocumentation$$DialogWindows$$PatScan$PatScan_b2.png]]		[[Image:GenDBWiki$$WebDocumentation$$DialogWindows$$PatScan$PatScan_b2.png]]

	This feature is available since GenDB version 2.4.		===This feature is available since GenDB version 2.4.===
	The exporter for the results of the pattern search is shown after clicking the '''Show exporting fields''' button. This button is only visible next to the '''Annotate''' button, if your status allows you to export data.		The exporter for the results of the pattern search is shown after clicking the '''Show exporting fields''' button. This button is only visible next to the '''Annotate''' button, if your status allows you to export data.
	You can choose the values, which should be exported, by clicking in the associated checkboxes.		You can choose the values, which should be exported, by clicking in the associated checkboxes.

imported>RobertSchmieder at 14:28, 28 March 2006

2006-03-28T14:28:16Z

← Older revision		Revision as of 16:28, 28 March 2006
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	== Interpretation of Results ==		== Interpretation of Results ==

	[[Image:GenDBWiki$$WebDocumentation$$DialogWindows$$PatScan$~~PatScan_b2~~.png]]		[[Image:GenDBWiki$$WebDocumentation$$DialogWindows$$PatScan$PatScan_b1.png]]

	The result shows the name of the region which the match belongs to, the position in the contig and the distance to the start of the region.		The result shows the name of the region which the match belongs to, the position in the contig and the distance to the start of the region.
Line 58:		Line 58:

	You can see that we specified a offset of 100 bases and filtered all matches which lie within the bounds of a region. As a result we get all intergenic matches which start at maximum 100 bases infront of a region. This can be very handy for identifying promotor regions.		You can see that we specified a offset of 100 bases and filtered all matches which lie within the bounds of a region. As a result we get all intergenic matches which start at maximum 100 bases infront of a region. This can be very handy for identifying promotor regions.

			== Exporter for Results ==

			[[Image:GenDBWiki$$WebDocumentation$$DialogWindows$$PatScan$PatScan_b2.png]]

			This feature is available since GenDB version 2.4.
			The exporter for the results of the pattern search is shown after clicking the '''Show exporting fields''' button. This button is only visible next to the '''Annotate''' button, if your status allows you to export data.
			You can choose the values, which should be exported, by clicking in the associated checkboxes.
			You also can choose the type of separation between '''tabulator''' (recommended) and '''comma'''.
			By clicking the '''Export values''' button, the export-file will be generated and a save dialog will be opened.

	== Q/A Troubleshooting ==		== Q/A Troubleshooting ==

imported>RobertSchmieder at 14:13, 28 March 2006

2006-03-28T14:13:45Z

← Older revision		Revision as of 16:13, 28 March 2006
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	{\| border="1" cellpadding="2" cellspacing="0"		{\| border="1" cellpadding="2" cellspacing="0"
	\| '''Options'''		\| '''Options'''
	\| Define the type of regions to be searched		\| Define the type of regions to be searched (DNA or Protein)
	\|-		\|-
	\|		\|

imported>RobertSchmieder at 14:08, 28 March 2006

2006-03-28T14:08:55Z

← Older revision		Revision as of 16:08, 28 March 2006
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	== Interpretation of Results ==		== Interpretation of Results ==

	[[Image:GenDBWiki$$WebDocumentation$$DialogWindows$$PatScan$~~PatScan_b~~.png]]		[[Image:GenDBWiki$$WebDocumentation$$DialogWindows$$PatScan$PatScan_b2.png]]

	The result shows the name of the region which the match belongs to, the position in the contig and the distance to the start of the region.		The result shows the name of the region which the match belongs to, the position in the contig and the distance to the start of the region.

imported>RobertSchmieder at 14:03, 28 March 2006

2006-03-28T14:03:39Z

← Older revision		Revision as of 16:03, 28 March 2006
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	PatScan is used to identify patterns in large sequences. It is possible to search patterns by specifying the number of insertions, deletions and substitutions or by defining a weight-matrix.		PatScan is used to identify patterns in large sequences. It is possible to search patterns by specifying the number of insertions, deletions and substitutions or by defining a weight-matrix.

	[[Image:GenDBWiki$$WebDocumentation$$DialogWindows$$PatScan$~~patscan1~~.png]]		[[Image:GenDBWiki$$WebDocumentation$$DialogWindows$$PatScan$PatScan_a.png]]

	The interface consists of 4 categories:		The interface consists of 4 categories:
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	== Interpretation of Results ==		== Interpretation of Results ==

	[[Image:GenDBWiki$$WebDocumentation$$DialogWindows$$PatScan$~~patscan2~~.png]]		[[Image:GenDBWiki$$WebDocumentation$$DialogWindows$$PatScan$PatScan_b.png]]

	The result shows the name of the region which the match belongs to, the position in the contig and the distance to the start of the region.		The result shows the name of the region which the match belongs to, the position in the contig and the distance to the start of the region.