Rice Genome Database
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"MapView" is the major data visualization tool in BGI-RISe. It provides a high level view of the sccaffolds (contigs) that make up the rice (Oryza sativa spp. indica (93-11) or Oryza sativa spp. japonica ( RGP ) )  genome assembly, of the genes, of the SNPs and other features that have been placed on it. And the users can switch to GeneView, cDNAView and other feature reports by clicking on the certain region.

 

The view of this page is split into three sections representing different levels of zooming into the chromosome:

  1. An Overview displaying the chromosome region
    (by default about 100Kb of DNA is shown)
  2. The main Contig View panel showing a range of features.
    (by default 10Kb of DNA is shown)
  3. A Base View panel showing the assembly sequence, quality values and SNPs to per base (by default 100bp of DNA is shown)

And followed by the Tracks with lots of items to the three sections.

The red boxes on the assembly in the Chromosome, Overview and Contig View panels represent the regions shown at higher magnification in the next panel below. The absolute base pair location of the region displayed in contig view is indicated in the navigator bar at the top of contig view. You can use this bar to navigate along any chromosome by entering a new chromosome and/or location.

 Overview:

The top chromosome panel displays an ideogram of the chromosome, showing the chromosoem number, the centromere, and the red box shows the region displayed in the overview panel below. The red box can be moved by clicking anywhere on the chromosome.

Below the chromosome panel are:

A scale bar

Homology blocks

SuperScaffold bands

Scaffold assembly map

Markers

BGF gene boxes

SNPs histogram.

 

Homology

Homology blocks shows perfect alignment to this region of the other species(indica or japonica). Hovering the mouse cursor over the homology block will bring up a float menu, where you can switch to the other subspecies (indica (93-11) or japonica (RGP)) by clicking the ?MapView:Homology(RGP/9311)? option.

 

SuperScaffoldl

(not shown by default)

SuperScaffold bands are assemblied from the scaffolds below, and user can click the band to jump to NCBI to see the more detailed information.

(Without to japonica(RGP))

 

Scaffold

The individual scaffolds of the genome assembly are shown in grass green. Where no grass green block is shown, there is a gap in the assembly. The name and orientation of the scaffold are shown in the block. The arrow represents the direction: => if the scaffold on the forward strand of the chromosome, <= if  the scaffold on the reverse strand of the chromosome. And if no space enough, there will only the orientation left or ever nothing left. The red box on the scaffold map shows the region displayed in the Contig View panel below. You can click anywhere on the scaffold map to move the red box.

(replaced by BAC to japonica(RGP))

 

Markers

Markers are shown in purple lines, followed by the marker name. Pointing the cursor to the marker will bring up a float menu, where the user can switch to the marker detailed page by cliciking the ?More Detailed:? option, or to the other subspecies (indica (93-11) or japonica (RGP)) by clicking the ?Japoncia(RGP)/Indica(9311) Mapview ? option.

 

BGFgenes

(not shown by default to this panel)

BGFgenes are shown in deep green boxes, and the alternating deep green block shows the exon. All BGFgenes predicted to this region are shown here regardles the orientations of the genes. Users can click the gene box to go to the GeneView page to see more precise strcuct and sequence information.

 

SNPs

SNPs indicate Single Nucleotide Polymorphisms and other sequence variations. The  X-coordinate of the histogram is averaged by 100, the Y-coordinate scales the number of the SNPs to the certain interval. The maxmium SNPs number of these intervals is as tall as the vertical coordinate, and the other colomns are shown proportionably. Hover the cursor on the SNPs colomn to see the start,end posion and the SNPs number of the interval, and click the colomn refresh this page to see details in the BaseView panel below.

 

Contig View:

The Contig View panel shows the chromosomal features in more detail and provides information concerning sequence annotations.

 

Navigation bar:

Clicking on one of these two buttons will move the whole display 1 Mb to the left or rigth.

Clicking on one of these two buttons will scroll the whole display to the left or right by the current display length.

Clicking on one of these buttons will zoom in and out the current display.

 

The scaffolds are again shown in grass green blocks, and the red box shows the region displayed in the Base View panel belowm, and click anywhere to move the red box.

 

The features of FL cDNAs, BACends, BGFgenes, FgeneSH, Repeats are shown above and under  the scaffold map. Those features above the scaffolds are positioned on the forward strand and those below are on the reverse strand.

 

FL cDNA

FL cDNAs indicate the Full length cDNAs, being shown the deep blue blocks. Those blocks belong to the same FL cDNA are linked by the broken lines. Hovering the cursor to the block will bring up a new float menu, where user can switch to cDNAView page of this cDNA by clicking the ?cDNAView:? option, or to the other subspecies MapView/cDNAView page according to this cDNA aligntment position by clicking the ?Japonica(RGP) [Indica(9311)] MapView / Japonica(RGP) [Indica(9311)] cDNAView? option.

 

Genes predicted

BGF genes are predicted by the software BGF(BGI Gene Finding). User can click the deep green box to go to the GeneView page to see more datails.

FgeneSH is vevy like the BGF, the only difference between them is that the FgeneSH genes are predicted by the software FgeneSH.

 

BACends

 

Repeats:

(not shown by default)

Regions of repetitive sequence are shown in the Repeats track. Tracks showing only certain classes of repeats can also be displayed. Most tracks are generated by running the program RepeatMasker. Point the mouse cursor to the repeat block brirng up the position information on the chromsome, and click the repeat element to jump to the repeat report page to see more details. Different colours of the block represent differ repeat types. The color to the type of the repeat table are below:

Class

Repeat type

Color

Class I?red??

LINE

SINE

Gypsy-like

Copia-like

Class II?green??

Ac/Ds TE

En/Spm TE

MULE

Class III ?blue??

Stowaway-like

Tourist-like

Unknown MITE

 

 

Contigs

(not shown by default)

 

Base View:

 

    BGI Last Modified 28 Oct, 2008     Feedback_
    Supported by China National Grid Project 2002AA104250