The display of comparative mapping data using ACEDB

# The Species Grid

A Species Grid shows all loci on a particular Map that have homologues in other species. As with many of the other comparative maps, homologies are drawn as small blue boxes. The y-coordinate of the homology box is the position on the single Map. The x-coordinate is the column midpoint of the second species involved in the homology. The name of the Map on which the locus in the second species is located is drawn to the right of the homology box.

The y-axis of the Species Grid is labelled with a chromosome (banding pattern) ideogram, should this be available, or by a numeric scale. If the former, then all chromosome band names will be shown and these may be double-clicked to bring up text information on the bands. In either case the Map name will be shown in bold black text and may be double-clicked to bring up its graphical display. The x-axis is labelled with all the relevant Map_set names. Each of these may be double-clicked. Upon this occurring, a text information box appears giving more information on the relevant Map_set.

The Species Grid shows the distribution of loci on a single Map in a particular species and their homologues throughout all other species (Map_sets) held within the database. Conserved segments between the first species and any of the other species should become apparent as vertical lines of blue homology boxes. If two adjacent loci in a particular column are located on the same Map in the second species, irrespective of the distance between them, they are joined by a vertical Magenta line. This is hoped to help in the identification of conserved segments. In the future, it is hoped that this will become an option that can be turned on or off by the user.

A special feature to highlight homology data across multiple species is built within the Species Grid. If the loci involved in a particular homology on a Species Grid are also involved in other homologies on the same Species Grid, then selecting the first homology (so that it is coloured light green) will cause all related homologies to be coloured red, the relationships between them becoming clear to the user.

A single click on a blue homology box causes the names of the two homologous loci to be displayed in the light blue header bar beneath the button menus. The box is then selected and is coloured light green. Any homology box may be double-clicked with the mouse. Upon this a text window appears giving information on the homology and on homologies of the two loci with loci from other species.

Two search facilities are provided, one for searching for an homology and one for a locus. If the text entered in either of these fields matches an homology or a locus that is present on the Species Grid, then the relevant homology box will be selected.

Button options available within the Species Grid are :

- Hide/Draw Chromosomes - toggles between a numeric scale on the y-axis and a banded chromosome ideogram, should this be available
- Highlight... - a menu giving various highlighting options
- Zoom in - increases the size of the graph
- Zoom out - decreases the size of the graph

Menu options available within the Species Grid are :

- Quit - destroys the Species Grid window
- Help - displays this help information
- Print - brings up the Print/Mail Selection tool
- Preserve - preserves the current Species Grid