Difference between revisions of "Gobe"

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[[Image:gobe-new.png|thumb|500px|New visualization of gobe]]
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[[Image:Gobe-interface.png|thumb|center|800px]]
  
[[Image:gobe-old.png|thumb|500px|Old visualization of gobe]]
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==What is Gobe?==
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Gobe is the name for the interface for [[GEvo]] that allows users interact with sequence alignments from multiple genomic regions. Gobe is written in Flash and requires the latest version of Adobe's [http://www.adobe.com/products/flashplayer/ Flash Player] to work.  Gobe allows uses to select regions of sequence similarity and will draw lines connecting those regions in order to identify and characterize patterns of genome evolution such as synteny, inversions, duplications, transpositions, insertions, and deletions.
  
Gobe is the name for the interface for GEvo that allows users interact with sequence alignments from multiple genomic regionsGobe is written in Flash and requires Adobe's [http://www.adobe.com/products/flashplayer/ Flash Player] to work. Gobe allows uses to select regions of sequence similarity and will draw lines connecting those regions in order to identify and characterize patterns of genome evolution such as synteny, inversions, duplications, transpositions, insertions, and deletionsGobe can be downloaded [gobe.googlecode.com here].
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==What do the graphics mean?==
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Please see examples [[GenomeView_examples | here.]]
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==How to use Gobe:==
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===Drawing Lines===
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* Click on a region identified as being similar to another region and a line or wedge is drawn connecting those regions
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* Hold shift the click (shift-click) on a region identified as being similar to another region and all regions for that comparison will have lines or wedges drawn
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* Clear lines and wedges by either clicking on a region of sequence similarity, the line or wedge, or find one of the "Clear Connector" buttons located above, below and in the information box
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===Changing title size===
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* Increase/Decrease the size of the genomic region titles by having the mouse of the flash viewer (aka the result graphics) and press the up/down arrow. <font color=red>Note:</font> You may need to first click on an HSP and draw a connecting wedge or line before Flash will register your up/down arrow key clicks.  Otherwise the browser appears to capture the event and scroll your window up and down.
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===Getting information===
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* Click on a genomic feature or a region of sequence similarity and a box will appear in which information about what you clicked on will also appear
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* You can drag resize this box.  When you click on something else, the box will get that information
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*Close the box by clicking on the "x" in the upper-right hand side of the box
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===Changing the extent of a genomic region===
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*Use the slider bars at the ends of the panels by clicking and dragging to board a sub-region to be analyzed
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==Download==
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Gobe can be downloaded [http://gobe.googlecode.com here].
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==Credits==
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Gobe is written and maintained by Brent Pedersen.
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==Brent has updated Gobe's visualization to use translucent wedges for connecting regions of sequence similarity, and a host of other improvements.==
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[[Image:Gobe-new-vis.png|thumb|center|600px|New translucent wedges for linking regions of sequence similarityResults can be recreated [http://tinyurl.com/loaalv here].]]
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[[Image:gobe-new.png|thumb|400px|New visualization of gobe]]
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[[Image:gobe-old.png|thumb|400px|Old visualization of gobe]]

Latest revision as of 20:56, 20 February 2010

Gobe-interface.png

What is Gobe?

Gobe is the name for the interface for GEvo that allows users interact with sequence alignments from multiple genomic regions. Gobe is written in Flash and requires the latest version of Adobe's Flash Player to work. Gobe allows uses to select regions of sequence similarity and will draw lines connecting those regions in order to identify and characterize patterns of genome evolution such as synteny, inversions, duplications, transpositions, insertions, and deletions.

What do the graphics mean?

Please see examples here.

How to use Gobe:

Drawing Lines

  • Click on a region identified as being similar to another region and a line or wedge is drawn connecting those regions
  • Hold shift the click (shift-click) on a region identified as being similar to another region and all regions for that comparison will have lines or wedges drawn
  • Clear lines and wedges by either clicking on a region of sequence similarity, the line or wedge, or find one of the "Clear Connector" buttons located above, below and in the information box

Changing title size

  • Increase/Decrease the size of the genomic region titles by having the mouse of the flash viewer (aka the result graphics) and press the up/down arrow. Note: You may need to first click on an HSP and draw a connecting wedge or line before Flash will register your up/down arrow key clicks. Otherwise the browser appears to capture the event and scroll your window up and down.

Getting information

  • Click on a genomic feature or a region of sequence similarity and a box will appear in which information about what you clicked on will also appear
  • You can drag resize this box. When you click on something else, the box will get that information
  • Close the box by clicking on the "x" in the upper-right hand side of the box

Changing the extent of a genomic region

  • Use the slider bars at the ends of the panels by clicking and dragging to board a sub-region to be analyzed


Download

Gobe can be downloaded here.

Credits

Gobe is written and maintained by Brent Pedersen.



Brent has updated Gobe's visualization to use translucent wedges for connecting regions of sequence similarity, and a host of other improvements.

New translucent wedges for linking regions of sequence similarity. Results can be recreated here.
New visualization of gobe
Old visualization of gobe