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| − | = Overview =
| + | please see [[EPIC-CoGe]] |
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| − | GenomeView is also known as the [[EPIC-CoGe]] genome browser that allows users to navigate genome sequence, annotation, and associated data tracks (quantitative measurements, SNPs, alignments, and markers).
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| − | More information, including video tutorials, can be found at [[EPIC-CoGe]].
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| − | = Navigation =
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| − | [[File:Screen Shot 2014-02-20 at 9.17.40 AM.png|thumb|left|600px]]
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| − | === Panning left-right ===
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| − | There are several ways to move along a genomic region:
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| − | *Click on the track and drag with mouse
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| − | *Use the left/right arrows located on the left of the viewer
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| − | *Click a location in the macro or micro coordinate bars at the top of the viewer.
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| − | *Enter a chromosome/start/end location in the location input bar at the top of the viewer.
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| − | === Zooming in and out ===
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| − | You can zoom into and out of a genomic region by:
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| − | *Click the (+) and (-) magnifying glass icons at the top of the viewer.
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| − | *Double-clicking on a region will zoom in one level
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| − | === Selecting Tracks ===
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| − | Use the track selector menu on the right of the viewer to add or remove tracks to the current view.
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| − | =What do the colors and glyphs mean=
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| − | See this page: [[GenomeView examples]]
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| − | = Getting additional information and data =
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| − | === Annotations ===
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| − | *Full Genomic Feature Annotations: Simply click on a feature, and a window will appear with the complete annotation for all features at that location. This window is resizeable and draggable. Please see [[Annotation information]], for more information about the information and links provided in this view.
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| − | *Popup-annotations: Select the "Pop-up Annotations" in the lower right hand part of the navigation screen, and the names of genomic features will pop-up when the mouse pointer hovers over them for a second. This window is resizable and draggable.
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| − | *Genome Information: Click on the "Genome Info" button in the lower left hand part of the navigation screen and an overview of the genome will pop-up.
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| − | <font color="red">Note:</font> many of the annotations contain links to other parts of CoGe. For example, if you want to get the sequence of a feature, just click on its location information in the pop-up annotation window.
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| − | === Grab Sequence ===
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| − | [[Image:GenomeView-get seq.png|thumb|center|600px]] To get genomic sequence in fasta format:
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| − | #Click "Grab Sequence" button in lower left of navigation screen.
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| − | #Click two regions in the genomic view to set the start and stop positions of the sequence you wish to grab.
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| − | #Click "View Sequence" to launch [[SeqView]] and get the sequence of the selected region in fasta format.
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| − | === Extract Genomic Features ===
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| − | [[Image:GenomeView-get feats.png|thumb|center|600px]] To genomic features:
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| − | #Click "Extract Features" button in lower left of navigation screen.
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| − | #Click two regions in the genomic view to set the start and stop positions of the sequence you wish to grab.
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| − | #Click "Get Features" to launch [[FeatList]] and get a list of all genomic features in the selected region.
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| − | = Understanding the image =
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| − | CoGe's genomic visualization library, [[GeLo]], permits the creation of a virtual chromosome using any style of glyphs to represent genomic information. Below are the common implementations used in CoGe
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| − | === Genomic Features ===
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| − | Genomic features are usually drawn as arrows or blocks of varying size and color. While there is some variation in how such features are drawn due to difference in how they were specified in the original data source (e.g. do mRNAs include introns?), the general conventions used in CoGe are:
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| − | *Grey (narrow): Gene. Usually starting at the beginning of the transcript, stopping at the end of the transcript, and including all intronic sequence, if appropriate.
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| − | *blue: mRNA transcript
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| − | *Green: CDS/protein coding regions (Please see note below)
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| − | *grey (large): RNA gene (tRNA, rRNA, etc.)
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| − | *orange-red: pseudogene
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| − | <font color="red">Note: </font>There are options in CoGe to color protein coding regions (CDS) based on the GC content of the wobble position in the codon. If this visualization is use, a color gradient is used to depict the wobble GC content such that:
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| − | *red: AT rich in CDS wobble positions
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| − | *green: GC rich in CDS wobble positions
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| − | *yellow: 50%/50% AT/GC in CDS wobble positions
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| − | === Background of virtual chromosome ===
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| − | The background of a genomic image can also be colored. Most often, this is used to color the genomic GC content such that:
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| − | *green: GC rich
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| − | *white: AT rich
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| − | *orange: Unsequenced (N)
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| − | *purple: masked sequenced (X). Masked genomes are generated often to remove repetitive sequence.
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| − | === Expanding overlapping genomic features ===
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| − | When genomic features overlap, as happens with alternatively spliced transcripts, you often have the option of drawn these on top of one another, or have CoGe detect this and drawn them above and below one another.
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| − | *Select "Expand Overlapping Gene Models" in the lower right of the screen to turn this on
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| − | === Examples and descriptions of GenomeView's visualization ===
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| − | As there are many different types of visualization, please follow this link: [[GenomeView examples]].
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| − | = Other options =
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| − | === Flat Gene Models ===
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| − | Flat gene models are simple arrows without the "tubular" design. This was the original way gene models were drawn before Josh Kane updated the model.
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| − | === Expand Gene Models ===
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| − | Separates genomic features that overlap at the same genomic position. Usually happens when alternatively spliced transcripts are annotated.
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| − | === Save Settings ===
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| − | Registered users can save which information they want to see by default as well as how gene models are drawn"
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| − | === Window Width ===
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| − | Sets the size of the window used for navigating a genomic region. Options in the top-left of navigation window
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| − | *Resize: sets the navigation window to the size specified in the "Window Width" box (in pixels)
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| − | *Full Screen: sets the navigation window to the size of the browser window
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| − | = Linking to GenomeView =
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| − | See [[Linking to GenomeView]] for information on how to link to GenomeView.
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| − | <br>
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| − | = Examples =
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| − | === Identifying Horizontal Gene Transfer using GC content in wobble position coloring ===
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| − | [[Horizontal Gene Transfer]]
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