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This page provides some information about how to interpret and understand the various graphic displays that acedb uses. For more information about acedb displays, read the quick guide to acedb at the official acedb web site. Please note that the acedb graphic display is only intended for viewing sequence, map, or loci objects. If you use it to view other items you will probably just see a graphic version of the standard acedb tree display.
TIP! Holding the mouse over any individual item in an acedb graphic display can often reveal more information about that item. If you are using Netscape this information will appear in the status bar at the bottom of your browser, if you are using Internet Explorer it will appear by the item that the mouse is being held over.
Acedb sequence displays
Below is an image of a sequence display for the AGR database.
As with all acedb databases, sequences are displayed vertically,
running 5' to 3' from top of the screen to the bottom. Features
associated with the sequence (e.g. exons, blast hits) are also
arranged vertically in columns. The central yellow bar represents the active part of the display. The ends
of the bar will sometimes be coloured blue if you are viewing a subsequence that
is part of a larger sequence. Adjacent to this bar is a scale bar (numbers
correspond to positions along the sequence - measured in base pairs). Immediately either side of this bar are predicted genes, on the left are genes
transcribed on the up strand, and on the right are genes transcribed on the down strand.
Exons are represented by hollow blue boxes, introns are represented by thin blue
lines connecting exons. Next to the genes come various coloured boxes representing BLAST matches to the
sequence you are viewing. These are colour coded to represent different types of
matches. This colour coding will vary for each individual database you are looking
at, but for AGR:
Clicking on exons or coding regions will take you to the sequence report page
for that individual coding region. Similarly, clicking on any BLAST homology
will take you to the sequence report page for the matching sequence. The sequence display might also show other information in the form of text.
You can click on the 'Zoom in..' or 'Zoom out..' buttons (at the top of the display)
to see more/less of the sequence. You can also click the 'DNA..' button to have the
DNA shown on the display (this will be done automatically for short sequences). Clicking
the 'Rev-Comp..' button reverses the orientation of the sequence. The other buttons
at the top of the display should not be used as they are not properly functional when
used via the web.
BLAST hits are sometimes arranged (depending on the database) into two separate
sections representing matches to each strand of the sequence. Within each section,
the arrangement of BLAST hits from left to right is an indicator of how good the
BLAST match is (matches with higher BLAST scores are shown further to the right of
the display). Holding the mouse
over any individual BLAST match will reveal the BLAST score (along with
details of the coordinates of the match).
Long sequences can often appear very cluttered and confusing when you try to view the whole
sequence at once. A quick way of navigating a long sequence (e.g. a BAC clone sequence)
is to click on a gene/predicted coding region in the region you are interested in. This will
take you to the 'AGR Sequence Report' page for that sequence. Then you can click on the
'Graphic Display' link at the top of the page to see a zoomed in view of just that subsequence.
You can then use the 'Zoom out..' button to see the region of sequence surrounding your gene
of interest. If you want to move to an adjacent gene, keep zooming out until the adjacent gene appears and then repeat the process.
Acedb map and loci displays
The default map image generated by AGR shows the middle portion of the map, i.e.
not all of the map is initially visible. The buttons:
allow the map to be zoomed or the whole map to be seen. Clicking on any marker
will centre the display around that marker, effectively scrolling the map. You should also
notice that clicking on a marker highlights that marker name on the map (the marker
name should appear in light blue). When a marker is selected you can then find out more
information about that marker, by clicking the 'Tree Display'
link at the top of the page. If no marker is selected and you click on the 'Tree Display' link
then you will see information about the map in general, rather than any specific marker.
The page that appears should always contain a list of all the individual markers that comprise
the map.
A green bar on a black line appears on all maps to indicate the proportion of the whole map which is currently being displayed. The example below would indicate that approximately the middle third of the chromosome is in view.
Below is an image of a physical map from the AGR database.
The scale on the left is an arbitrary scale relating to the position of an object on the chromosome. Probes and recombinant inbred markers are shown in yellow. On the far right (in black) are all of the overlapping clones that are known in that region. Clones that have associated EMBL sequences are shown in the middle. Clicking on a marker re-centres the map on that marker. All other objects (clones, sequences, etc.) can be clicked to retrieve more information
The highlighting in this images indicates the association between the sequence EMBL:AL049751 and the sequenced clone F17N18.
Below is an image showing part of a recombinant inbred (RI) map from the AGR database.
The scale on the left refers to the genetic map position in centiMorgans (cM). Markers are colour coded according to the confidence of their placement: Backbone marker, Single position or Best of Multiple positions. The Arabidopsis Genome Initiative (AGI) clones that are shown on the right, are fixed by "Nearest registered RI marker" information from the TAIR database.
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Page last modified: Wednesday, 14-Mar-2001 13:51:03 GMT
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