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| [[Image:GenomeView.png|thumb|right|800px|Interface to GenomeView]]
| | please see [[EPIC-CoGe]] |
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| =Navigation=
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| [[Image:GenomeView-navigation.png|thumb|600px|center|GenomeView Navigation]]
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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 chromosome and drag with mouse
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| *Use the left/right arrows located on the left of the viewer
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| *Use scroll bar below graphics by clicking and dragging, or clicking somewhere in the bar
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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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| *Using navigation menu on the left of the viewer. (+) zooms in, (-) zooms out, and the tick-marks take you a specific zoom level.
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| *Double-clicking on a region will zoom in one level
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| *Use the mouse scroll-wheel to zoom in and out if the mouse pointer is over the chromosome
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| ===Changing displayed information===
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| There are often many types of genomic information that can be displayed as overlays. To toggle various overlays, open the overlay menu by clicking on the "+" symbol in the top right corner of the viewer and select the overlays you wish to view.
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| =Getting additional information and data==
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| ==Annotations==
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| ===Full Annotations===
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| ===Popup-annotations
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| ==Grab Sequence==
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| ==Extract Genomic Features==
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| ==Other options==
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| ===Flat Gene Models===
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| ===Expand Gene Models===
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| =Understanding the image=
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| [[Image:GenomeView-background.png|thumb|500px|Background of chromosome colored green to show GC rich regions]]
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| [[Image:GenomeView-gene.png|thumb|500px|Gene models drawn as gray arrows]]
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| [[Image:GenomeView-mRNA.png|thumb|500px|mRNA drawn as blue arrows (on top of gray genes)]]
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| [[Image:GenomeView-CDS.png|thumb|500px|Protein coding regions (CDS) drawn as green arrows (on top of gray genes and blue mRNAs)]]
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| [[Image:GeLo-example.png|thumb|500px|Overlapping genomic features are detected and expanded to show alternatively spiced transcripts]]
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| [[Image:GenomeView-Unsequenced.png|thumb|500px|Genomic region with unsequenced regions colored orange from the genome of Carica papaya]] | |
| [[Image:GenomeView-masked.png|thumb|500px|Genomic region with masked sequence colored purple]]
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| [[Image:GenomeView-rRNA.png|thumb|500px|Microbial (archaea) genomic region with 23S and 16S rRNA genes drawn as wide gray arrows]]
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| [[Image:GenomeView-pseudogene-2.png|thumb|500px|Microbial (archaea) genomic region with many pseudogenes drawn as orange-red arrows]]
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| [[Image:GenomeView-wobbleGC1.png|thumb|500px|Wobble GC content colored for Chlamydomonas reinhardtii genome. Green means high GC content in codon wobble positions]]
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| [[Image:GenomeView-wobbleGC2.png|thumb|500px|Wobble GC content colored for Chlamydomonas reinhardtii chloroplast genome. Red means low GC content in codon wobble positions]]
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| [[Image:GenomeView-wobbleGC3.png|thumb|500px|Wobble GC content colored for Chlamydomonas reinhardtii mitochondria genome. Yellow means ~50% GC content in codon wobble positions]]
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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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| *purple: masked sequenced (X). Masked genomes are generated often to remove repetitive sequence.
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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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| ==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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