Pattern Discovery - Revision history

Smith: /* Details as Hover Text */

2015-01-27T02:39:04Z

‎Details as Hover Text

Smith: /* Versions prior to geWorkbench 2.3.0 */

2015-01-27T02:35:25Z

‎Versions prior to geWorkbench 2.3.0

Smith: /* Single Pattern */

2015-01-27T02:32:12Z

‎Single Pattern

Smith: /* Discovery Session Server */

2015-01-27T01:41:53Z

‎Discovery Session Server

Smith: /* Discovery Session Server */

2015-01-27T01:30:56Z

‎Discovery Session Server

Smith at 23:55, 22 January 2014

2014-01-22T23:55:04Z

Smith: /* Position Histogram */

2014-01-17T17:52:42Z

‎Position Histogram

Smith: /* Position Histogram */

2014-01-17T17:51:28Z

‎Position Histogram

Smith: /* Options to Save or Mask Patterns */

2012-11-14T23:29:23Z

‎Options to Save or Mask Patterns

Smith: /* Exhaustive tab */

2012-07-12T15:23:00Z

‎Exhaustive tab

← Older revision		Revision as of 02:39, 27 January 2015
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	[[Image:PatternDiscovery_Basic_Histones_Result_exact_3_hover.png]]		[[Image:PatternDiscovery_Basic_Histones_Result_exact_3_hover.png]]
		+
		+
		+	The result of a different search using the BLOSUM50 substitution matrix shows the regular expression in the hover text as well as the sequence location in the detail strip below:
		+
		+
		+	[[Image:Pattern_discovery_sequence_tooltip3.png]]

	===Result (Exact matches) full sequence view===		===Result (Exact matches) full sequence view===

← Older revision		Revision as of 02:35, 27 January 2015
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	The results of repeating the same run as before but using BLOSUM50 are pictured above in '''Viewing Results'''.		The results of repeating the same run as before but using BLOSUM50 are pictured above in '''Viewing Results'''.

−
−
−	~~==Versions prior to geWorkbench 2.3.0==~~
−	~~===Layout===~~
−	~~The Pattern Discovery component had a different layout prior to release 2.3.0. The controls and results viewing were placed together.~~
−
−	~~The Pattern discovery component control area had three sections.~~
−	~~# Run controls are shown at top,~~
−	~~# the hit display area is in the center (empty in the figure below), and~~
−	~~# the parameter settings are at bottom.~~
−
−	~~[[Image:PatternDiscovery_Params_Basic_Norm.png]]~~
−
−	~~===Top-level run controls===~~
−
−	~~[[Image:PatternDiscovery_Run_Controls.png]]~~
−
−	* '''Normal''' - select the "normal" pattern discovery algorithm.
−	* '''Exhaustive''' - select the "exhaustive" pattern discovery algorithm. This takes much more time.
−
−	* '''Curling arrow''' - start a new pattern discovery run.
−	* '''Stop sign''' - Cancel the current pattern discovery run
−	* '''File folder''' - load a pattern file
−
−	* '''Progress bar''' - To the right of the control buttons is a progress bar that reports on the current stage of discovery being executed.

← Older revision		Revision as of 02:32, 27 January 2015
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	The position of matches along the sequence are shown using colored boxes (here blue).		The position of matches along the sequence are shown using colored boxes (here blue).
		+
		+	If a given sequence hit is clicked, it will appear in the horizontally scrollable detail view below.

← Older revision		Revision as of 01:41, 27 January 2015
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−	[[Image:~~PatternDiscovery_UploadProgressBar~~.png]]	+	[[Image:PatternDiscovery_RunningProgressBar.png]]

	==Viewing results==		==Viewing results==

@@ Line 95: / Line 95: @@
-The progress bar will show the sequence upload and run steps:
+The progress bar will show the sequence upload:
-[[Image:PatternDiscovery_ProgressBar.png]]
+[[Image:PatternDiscovery_UploadProgressBar.png]]
 ==Viewing results==

@@ Line 12: / Line 12: @@
 Exhaustive Discovery starts from a relatively high minimum support (e.g. patterns occurring in 75% of the sequences) and it progressively reduces the support, until a statistically significant pattern is discovered. Discovered patterns are reported and then masked in the sequence set so that they are no longer discovered. Then the process continues iteratively until the minimum support reaches a lower user-defined limit. Exhaustive Discovery, thus, produces a list of non-overlapping motifs in order of support.
-The Pattern Discovery component is available when a sequence (FASTA format) file has been loaded in the Project Folders component, and its data node is selected.
+The Pattern Discovery component is available when a sequence (FASTA format) file has been loaded in the [[Workspace]], and its data node is selected.
@@ Line 111: / Line 111: @@
 * '''Sequences Hit''' - The number of sequences which contained at least one occurrence of the discovered motif.
 * '''# of Tokens''' - the number of full-character tokens in the motif.
-* '''ZScore''' - a measure of how often the motif would be found in a random set of sequences of the same size and composition as the project dataset.
+* '''ZScore''' - a measure of how often the motif would be found in a random set of sequences of the same size and composition as the current dataset.
 * '''Motif''' - a sequence of tokens, which may be full characterd or wildcard.
 ** A period (.) represents a wildcard and matches any character.
@@ Line 170: / Line 170: @@
 * '''Step''' - the sequences are divided into bins of the specified "step" size.  The step size is entered as an integer.
 * '''Plot Position''' - push to draw a new histogram.
-* '''Image snapshot''' - place a copy of the histogram as an image into the Project Folders component.
+* '''Image snapshot''' - place a copy of the histogram as an image into the [[Workspace]].
@@ Line 179: / Line 179: @@
 [[Image:PatternDiscovery_Basic_Histones_Result_exact_3_histogram.png]]
-==Adding results to the Projects Folder==
+==Adding results to the Workspace==
-The results of a run of '''Pattern Discovery''' are automatically placed in the Project Folder:
+The results of a run of '''Pattern Discovery''' are automatically placed in the [[Workspace]]:
@@ Line 224: / Line 224: @@
 # Make sure that Pattern Discovery and Position Histogram (if desired) are loaded in the Component Configuration Manager.
-# Load a file containing the sequence or sequences to be analyzed into the Project Folders component.
+# Load a file containing the sequence or sequences to be analyzed into the [[Workspace]].
 For this example, we use a file containing a number of histone sequences, [[Media:H1H5_HistoneDB_NHGRI.fasta | H1H5_HistoneDB_NHGRI.fasta]].

@@ Line 165: / Line 165: @@
 The Position Histogram displays (binned) support of each motif along the length of the sequences.
-* Support - Out of all occurrences of a particular pattern, the percentage that start within the bin beginning at a particular location.
+* '''Support''' - Out of all occurrences of a particular pattern, the percentage that start within the bin beginning at a particular location.
 * '''Step''' - the sequences are divided into bins of the specified "step" size.  The step size is entered as an integer.

← Older revision		Revision as of 23:29, 14 November 2012
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	* '''Save All Patterns''' - This will save both all of the patterns and their hits to the query sequences. The locations positions on the query sequences) saved are specific to the particular input file used. The name of this file is saved in the pattern file.		* '''Save All Patterns''' - This will save both all of the patterns and their hits to the query sequences. The locations positions on the query sequences) saved are specific to the particular input file used. The name of this file is saved in the pattern file.
		+
		+	'''Note''' - for the last two options, the location of the sequence hit is indicated relative to the position of the sequence in the list of sequences actually searched. If only a subset of sequences were active (a marker set was activated in the Markers component), then the position recorded is relative to the sequence order in this subset. However, if the marker set is subsequently deactivated and the saved pattern file reloaded from disk, it will still match against the proper sequences. The sequence line numbers recorded in the file are not used.

@@ Line 45: / Line 45: @@
 * '''Decrement support (%)''' - sets the size of intervals by which support level is decreased in successive searches (default is 5).  The decrease is multiplicative, e.g. if one enters 5%, support will be reduce to 95% of its previous value at each step.
 * '''Minimum Support (Number of Sequences)''' - sets the lower limit on the number of sequences that must contain a specific motif (default is 10).
-** '''Note''' - In versions of geWorkbench prior to 2.2.1, if a % sign is included in the minimum support text field, the percentage entered will be applied to the initial minimum support value.  For example, if the initial minimum support is 70%, and "10%" is entered in this field, the final stopping value for the calculation will be 7%.
+** '''Note''' - In versions of geWorkbench prior to 2.2.1, if a % sign was included in the minimum support text field, the percentage entered was applied to the initial minimum support value.  For example, if the initial minimum support was 70%, and "10%" is entered in this field, the final stopping value for the calculation would be 7%.
 * '''Minimum Pattern Number''' - sets a lower limit on the number of motifs in a cluster (point at which support decrease stops).