Chromosome Browser help
Last Updated: 22 August 2008
The Chromosome browser shows aligments of sequence scaffolds to polytene chromosome maps for Muller elements of the sequenced Drosophila species. The chromosome maps are based on the ones publised in Schaeffer et. al., Genetics 179: 1601-1655 2008, and the well characterised physical and genetic maps for Drosophila melanogaster (see Bridges, 1935, Bridges, 1938, Lefevre, 1976, Lindsley and Zimm, 1992 and the Map Conversion Table). Each of the aligned sequence scaffolds, shown in blue, provides access to the sequence data and gene models in that region. When you move your cursor over one of the blue scaffolds a yellow box appears that corresponds to a GBrowse window. Clicking on the yellow box will take you to the corresponding location in GBrowse. The precise location represented by the box appears under "Location" at the top right of the screen and this information is updated when you move the mouse to the right or the left within the scaffold.
Species can be selected from a drop down menu at the top left hand side of the page. When you return to the page the last species you viewed will be displayed unless you have cleared your cookies.
Maximum GBrowse Window
This control allows you to set the maximum size of the GBrowse window. It will take longer for GBrowse to display a sequence interval of 500Kb than 50Kb, however 50Kb may not be a large enough interval to locate a gene from its cytological position. We recommend starting with a maximum interval of 200Kb.
You may notice that on some maps the size of the GBrowse window varies between scaffolds due to the different scales of the physical and polytene chromosome maps. However, unless the size of the scaffold is less than the GBrowse window setting, the yellow box will represent the maximum interval selected.
The current scaffold number and sequence location shown as a range covering the interval highlighted, for example scaffold_13417:2762382..2812382, is indicated in this box when the mouse cursor is placed over a blue sequence scaffold. The scaffold numbers relate to release 5 of the sequence for Drosophila melanogaster, release 2 for Drosophila pseudoobscura pseudoobscura, and release 1 for the other species.
You can use the arrows at the top left hand corner of the maps to move around, or alternatively place you cursor over the map and drag on the surface of the map. The "Center" button allows you to rapidly return to the middle of the map. You can also move around the map by dragging on the blue box shown in the overview map at the bottom right hand corner of the map window.
The map can be enlarged or shrunk by clicking on the "+" and "-" buttons found under the arrow keys in the top left hand corner of the map. Maps for different Muller Elements can be viewed by using the controls at the top right of the map. Please see the Muller Element Arm Synteny Table for more information on the syntenic relationships among the 12 sequenced genomes, their standard chromosomal numbering and corresponding Muller element. This table can be accessed while viewing a map by pressing the "Synteny" button, and links within the table provide an another way of navigating between maps.
D.erecta, D.sechellia, D.simulans and D.yakuba maps
These sequenced species are so similar to Drosophila melanogaster that the sequence scaffolds were aligned to combined Bridges' ideogram and Lefevre photographic maps. The position of inversion breakpoints are indicated by red lines with arrowheads.
The sequence scaffolds are aligned to ideograms and photographic maps of the respective species. With the exception of Drosophila grimshawi these maps also include genetic maps above the aligned scaffolds. Lines are drawn between the maps to show how they relate to one another. Please note that these lines are only approximate. There are no maps for the Muller F elements of Drosophila ananassae, Drosophila pseudoobscura, Drosophila persimilis or Drosophila mojavensis, because although scaffolds were assigned to the elements the orientation of the sequence data is uncertain.