Description
This track shows locations of Sequence Tagged Site (STS) markers
along the draft assembly. These markers have been mapped using either
genetic mapping (Genethon, Marshfield, and deCODE maps), radiation
hybridization mapping (Stanford, Whitehead RH, and GeneMap99 maps) or
YAC mapping (the Whitehead YAC map) techniques. Since August 2001,
this track no longer displays fluorescent in situ hybridization (FISH)
clones, which are now displayed in a separate track.
Genetic map markers are shown in blue; radiation hybrid map markers
are shown in black. When a marker maps to multiple positions in the
genome, it is shown in a lighter color.
Methods
Positions of STS markers are determined using both full sequences
and primer information. Full sequences are aligned using blat,
while isPCR (Jim Kent) and ePCR are used to find
locations using primer information. Both sets of placements are
combined to give final positions. In nearly all cases, full sequence
and primer-based locations are in agreement, but in cases of
disagreement, full sequence positions are used. Sequence and primer
information for the markers were obtained from the primary sites for
each of the maps, and from UniSTS.
Using the Filter
The track filter can be used to change the color or include/exclude
a set of map data within the track. This is helpful when many items
are shown in the track display, especially when only some are relevant
to the current task. To use the filter:
- In the pulldown menu, select the map whose data you would like to
highlight or exclude in the display. By default, the "All
Genetic" option is selected.
- Choose the color or display characteristic that will be used to
highlight or include/exclude the filtered items. If
"exclude" is chosen, the browser will not display data from
the map selected in the pulldown list. If "include" is
selected, the browser will display only data from the selected map.
When you have finished configuring the filter, click the
Submit button.
Credits
This track was designed and implemented by Terry Furey. Many
thanks to the researchers who worked on these maps, and to Greg
Schuler, Arek Kasprzyk, Wonhee Jang, and Sanja Rogic for helping
process the data. Additional data on the individual maps can be found
at the following links:
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