Some documentation on the features of the new GMAP display is now online. Working examples of these features have now been exported from the C. elegans database into mapdb, which you can run at /disk2/demos/sunos/mapdb.
Jo Dicks has now ported her Comparative Maps displays into ace version 4. You can see these by running /disk2/demos/sunos/oxmapdb4.
To get started, try this:
- Choose "Oxford Grid 2" from the main menu.
- Enter "rice" and "zea" as the Map_sets to be compared.
- Click twice in the rectangle for Zea-Ahn-1 x Rice-CU-3 to see the list of homologous locus pairs.
- Choose "Pairmap" from the dropdown menu for that rectangle to see the dotplot of actual locations of these homologies.
These displays are still under development. The items in the Main Menu that work already are "Oxford Grid", "Species Grid", and "Translocation Grid". "GridMap" is meant to be a more general interface to specifying what to compare and how to display it, but isn't running yet. Watch this space for further developments.
See the wonderful documentation of the GMAP magic tags from Sam Cartinhour and Simon Kelley, for ?Map, and for ?Locus and other mappable objects.
For an introduction to Arun Aggarwal's new integrated map/sequence
display, click
here.
To look at a live version, run /disk2/demos/sunos/syn3.3. Illustrative
objects to look at are
- Map 21.LBL
- Clone LBLHP1-0005
- Clone h8-9_b7
- Assembly h8-9_b7-Ass1
- To see how syntenic loci are tied together in the display, look at Locus
S100B.
For an introduction to this display. This code is currently in the process of being folded into the ACEDB 4-0 distribution. To watch the progress look at /disk2/demos/sunos/syn4.0.
For examples of using the Anchor tag in the MultiMap, to tie together Locus objects whose names are not the same, run /disk2/demos/sunos/mapdb. Mapdb is a sample database to contain working illustrations of the features of the map displays.
To see some additional MultiMap examples from Octobase, the human chromosome 8 database, look at /disk2/demos/sunos/octodemo4.0.
Members of the Mapping Tools Working Group: Dave Matthews Chair MultiMap Simon Kelley Ace programmer Genetic map Arun Aggarwal Jr. Ace programmer Physical map Joanne Dicks ApprentAce programmer MultiMap Richard Bruskiewich Evaluator MultiMap Nancy Caraher Evaluator Physical map Karen Davis Evaluator Genetic map Doug Smith Evaluator Physical map Natassa Spiridou Evaluator Genetic map